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PubMed2000

Stability and evolution of overlapping genes.

When the same sequence of nucleotides codes for regions of more than one functional polypeptide, this sequence contains overlapping genes. Overlap is most common in rapidly evolving genomes with high mutation rates such as viruses, bacteria, and mitochondria. Overlap is thought to be important as: (1) a means of compressing a maximum amount of information into short sequences of structural genes; and (2) as a mechanism for regulating gene expression through translational coupling of functionally related polypeptides. The stability of overlapping codes is examined in relation to the information cost of overlap and the mutation rate of the genome. The degree of overlap in a given population will tend to become monomorphic. Evolution toward partial overlap of genes is shown to depend on a convex cost function of overlap. Overlap does not evolve when expression of overlapping genes is mutually exclusive and produced by rare mutations to the wild-type genome. Assuming overlap increases coupling between functionally related genes, the conditions favoring overlap are explored in relation to the kinetics of gene activation and decay. Coupling is most effective for genes in which the gene overlapping at its 5' end (leading gene) decays rapidly, while the gene overlapping at the 3' end (induced gene) decays slowly. If gene expression can feedback on itself (autocatalysis), then high rates of activation favor overlap.

Evolution, Molecular↗
PubMed1993

Genome organization of the sigma rhabdovirus: six genes and a gene overlap.

The sequence of the sigma virus glycoprotein gene has been reported. We report here the cloning of the cDNAs to four other genes, their physical map on the genome, the sequencing of the intergenic regions, and the determination of the gene junction signals. This analysis reveals unusual traits for a rhabdovirus: four genes map upstream of the glycoprotein gene and the glycoprotein gene overlaps the upstream gene by 33 nucleotides. Northern analysis did not show bicistronic transcripts of the overlapping genes, whereas it revealed bicistronic transcripts of two genes which are separated by a stretch of six nucleotides. This leads us to reconsider the significance of rhabdovirus consensus gene-end sequences and to integrate these data into the models proposed for polymerase functioning.

Amino Acid Sequence↗
PubMed1996

cDNA cloning and chromosomal localization of the genes encoding the alpha- and beta-subunits of human Rab geranylgeranyl transferase: the 3' end of the alpha-subunit gene overlaps with the transglutaminase 1 gene promoter.

We have isolated and sequenced the complete coding sequences of the human genes for the alpha- and beta-subunits of Rab geranylgeranyl transferase (Rab GGTase). The alpha- and beta-subunit genes code for proteins of 567 and 331 amino acids, respectively, showing 91 and 95% amino acid identity to their rat counterparts. We employed fluorescence in situ hybridization to map the beta-subunit gene to human chromosome 1p31. The alpha-subunit gene could be assigned to 14q11.2, less than 2 kb upstream of the transcription initiation site of the gene for transglutaminase 1 (TGM1). The two genes are arranged in tandem in a head-to-tail orientation. The short intergenic sequence between the two loci contains several promoter elements that are involved in the induction of TGM1 gene expression in squamous cells. These results suggest that cis-acting factors for cell-type-specific transcription of one gene are located within the transcribed region of a functionally unrelated gene.

Alkyl and Aryl Transferases↗
PubMed2002

Male-enhanced antigen-1 gene flanked by two overlapping genes is expressed in late spermatogenesis.

The male-enhanced antigen-1 gene (Mea1) was originally isolated from a murine testicular cDNA library using anti-H-Y antigen antisera and was assigned to chromosome 17. On analysis of its structure and expression, we found that the Mea1 genomic sequence is flanked by two other genes: Ppp2r5d present in its 3'-terminus in a tail-to-tail orientation and a novel gene called Peas in its 5'-terminus in a head-to-head orientation. The coding sequences of the two genes embedded in the Mea1 sequence are located on the opposite DNA strands of Mea1. Cap-site analysis of Mea1 revealed that it is transcribed from at least seven sites. Most splice variants of Mea1 were abundantly expressed in the testis; the d-type was weakly expressed in the other tissues. AP-2-binding motifs were detected in the transcription-initiation sites. In situ hybridization and immunohistochemical studies revealed Mea1 expression in pachytene spermatocytes. This expression was most prominent in spermatids and residual bodies. The Mea1 protein was also localized in the cytoplasm of elongated spermatids and residual bodies. Localization of the Mea1 suggests that it may function in the very late stages of spermiogenesis. The possibility that Mea1 is one of the serologically detectable male antigens is discussed.

Alternative Splicing↗
PubMed1994

Controlled expression and structural organization of a Lactococcus lactis bacteriophage lysin encoded by two overlapping genes.

The phi vML3 bacteriophage lysin is specific for lactococci and could be used to promote enzyme release during cheese manufacture. The level of lysin expression from the cloned gene using its own upstream sequences is very low. Expression in Escherichia coli by using a synthetic hybrid lysin gene and a series of BAL 31 deletions of the original cloned DNA fragment suggested that the start of the gene had previously been incorrectly assigned. Reevaluation of homology between the lysin and Bacillus subtilis PZA protein 15 led to the identification of a new potential ribosome binding site (RBS). A 0.72-kb PCR-generated fragment including this RBS and the complete lysin gene was expressed and inducibly controlled. The translational start of the lysin gene was identified as an isoleucine codon, and this may lead to a low translation rate. During the analysis of the BAL 31 deletion fragments, two proteins of 20 and 8 kDa were shown to be expressed from the originally defined lysin gene. The DNA sequence has a second open reading frame with a good RBS and two potential start methionines. The smaller lysin protein was isolated, and the N terminus was sequenced, confirming that one methionine codon acted as the start of a second gene. The larger lysin protein has homology with lysozymes. The smaller lysin protein has some features resembling those of a holin. The possible roles of these two proteins in lysis of lactococci are discussed.

Amino Acid Sequence↗
PubMed1999

Functional anatomy of herpes simplex virus 1 overlapping genes encoding infected-cell protein 22 and US1.5 protein.

Earlier studies have shown that (i) the coding domain of the alpha22 gene encodes two proteins, the 420-amino-acid infected-cell protein 22 (ICP22) and a protein, US1.5, which is initiated from methionine 147 of ICP22 and which is colinear with the remaining portion of that protein; (ii) posttranslational processing of ICP22 mediated largely by the viral protein kinase UL13 yields several isoforms differing in electrophoretic mobility; and (iii) mutants lacking the carboxyl-terminal half of the ICP22 and therefore DeltaUS1.5 are avirulent and fail to express normal levels of subsets of both alpha (e.g., ICP0) or gamma2 (e.g., US11 and UL38) proteins. We have generated and analyzed two sets of recombinant viruses. The first lacked portions of or all of the sequences expressed solely by ICP22. The second set lacked 10 to 40 3'-terminal codons of ICP22 and US1. 5. The results were as follows. (i) In cells infected with mutants lacking amino-terminal sequences, translation initiation begins at methionine 147. The resulting protein cannot be differentiated in mobility from authentic US1.5, and its posttranslational processing is mediated by the UL13 protein kinase. (ii) Expression of US11 and UL38 genes by mutants carrying only the US1.5 gene is similar to that of wild-type parent virus. (iii) Mutants which express only US1. 5 protein are avirulent in mice. (iv) The coding sequences Met147 to Met171 are essential for posttranslational processing of the US1.5 protein. (v) ICP22 made by mutants lacking 15 or fewer of the 3'-terminal codons are posttranslationally processed whereas those lacking 18 or more codons are not processed. (vi) Wild-type and mutant ICP22 proteins localized in both nucleus and cytoplasm irrespective of posttranslational processing. We conclude that ICP22 encodes two sets of functions, one in the amino terminus unique to ICP22 and one shared by ICP22 and US1.5. These functions are required for viral replication in experimental animals. US1.5 protein must be posttranslationally modified by the UL13 protein kinase to enable expression of a subset of late genes exemplified by UL38 and US11. Posttranslational processing is determined by two sets of sequences, at the amino terminus and at the carboxyl terminus of US1.5, respectively, a finding consistent with the hypothesis that both domains interact with protein partners for specific functions.

Amino Acid Sequence↗
PubMed2005

Comparative study of overlapping genes in bacteria, with special reference to Rickettsia prowazekii and Rickettsia conorii.

Overlapping genes have been proposed as a means of achieving genome reduction by compressing the maximum amount of information in limited sequence space. In this report, comparative analyses of the overlapping genes of genomes of nine bacteria with different lifestyles were performed. The results clearly suggest that overlapping genes may be a result of evolutionary pressure to minimize genome size. The genomes of two closely related obligatory intracellular parasites - Rickettsia prowazekii and Rickettsia conorii - were investigated further. Detailed analyses of these two genomes revealed that mutations at the ends of coding regions and elimination of intergenic DNA are the main forces that determine overlapping of genes.

Biological Evolution↗
PubMed2001

Overlapping genes in parasitic protist Giardia lamblia.

The parasitic protist Giardia lamblia lacks mitochondria and peroxisomes, as well as many typical membrane-bound organella characteristics of higher eukaryotic cells, together with extremely economized usage of DNA sequence, as demonstrated by the lack of introns. We describe here the presence of overlapping genes in G. lamblia, in which a part of the protein coding sequence of one mRNA exists in a region corresponding to the 3'-noncoding region of another mRNA transcribed from a gene on the opposite strand. Recently we isolated 13 kinesin-related cDNAs from G. lamblia. Nine of these cDNAs contain long 3'-noncoding sequences in which long open reading frames (ORFs) exist (in the remaining four cDNAs, the lengths of the 3'-noncoding sequences are very short). The predicted amino acid sequences of these ORFs were subjected to a search for homologies with sequences in databases. The amino acid sequences of the six ORFs exhibited significant sequence similarities with known sequences. These lines of evidence suggest the frequent occurrence of gene overlap in Giardial genome.

Animals↗
PubMed1989

Overlapping genes of Drosophila melanogaster: organization of the z600-gonadal-Eip28/29 gene cluster.

The Drosophila gonadal (gdl) gene is a member of a gene cluster that maps cytogenetically to the 71CD interval of chromosome 3. The gene is bordered distally by z600, a gene expressed predominantly during early embryogenesis, and proximally by Eip28/29, a gene regulated by ecdysone in Drosophila cell lines. gdl can be expressed in either of two modes in adults: gdlF expression leads to the transcripts 1300 and 1000, which are found in the ovaries, whereas gdlM expression leads to the transcripts 1500 and 1200, which are found in the testes. In situ hybridization analysis reveals that this expression occurs in the germ line during oogenesis and spermatogenesis. Structural studies identify an unusual gdl sequence organization. The ovarian and testes transcripts differ at their 5' ends because of the utilization of different transcription initiation sites. This result indicates that alternative promoter usage is responsible for sex-specific gdl expression. Within an expression mode, the two transcripts differ at their 3' ends as a result of multiple polyadenylation site usage; one of these sites resides within the 5' exon of the Eip28/29 gene. gdl is overlapped by z600 as well because the z600 transcript is polyadenylated at position +91 of the gdlM transcripts. An analysis of germ-line transformants reveals that gdl can be expressed properly outside the overlapping gene environment because a 1.8-kb DNA region contains all the sequences necessary for gdl sex-specific expression.

Animals↗
PubMed1997

On the informational content of overlapping genes in prokaryotic and eukaryotic viruses.

In genetic language a peculiar arrangement of biological information is provided by overlapping genes in which the same region of DNA can code for functionally unrelated messages. In this work, the informational content of overlapping genes belonging to prokaryotic and eukaryotic viruses was analyzed. Using information theory indices, we identified in the regions of overlap a first pattern, exhibiting a more uniform base composition and more severe constraints in base ordering with respect to the nonoverlapping regions. This pattern was found to be peculiar to coliphage, avian hepatitis B virus, human lentivirus, and plant luteovirus families. A second pattern, characterized by the occurrence of similar compositional constraints in both types of coding regions, was found to be limited to plant tymoviruses. At the level of codon usage, a low degree of correlation between overlapping and nonoverlapping coding regions characterized the first pattern, whereas a close link was found in tymoviruses, indicating a fine adaptation of the overlapping frame to the original codon choice of the virus. As a result of codon usage correlation analysis, deductions concerning the origin and evolution of several overlapping frames were also proposed. Comparison of amino acid composition revealed an increased frequency of amino acid residues with a high level of degeneracy (arginine, leucine, and serine) in the proteins encoded by overlapping genes; this peculiar feature of overlapping genes can be viewed as a way with which they may expand their coding ability and gain new, specialized functions.

Amino Acid Sequence↗
PubMed1993

Tenascin-X: a novel extracellular matrix protein encoded by the human XB gene overlapping P450c21B.

A human gene termed XB overlaps the P450c21B gene encoding steroid 21-hydroxylase and encodes a protein that closely resembles extracellular matrix proteins. Sequencing of phage and cosmid clones and of cDNA fragments shows that the XB gene spans 65 kb of DNA, consisting of 39 exons that encode a 12-kb mRNA. The predicted protein of over 400 kD consists of five distinct domains: a signal peptide, a hydrophobic domain containing three heptad repeats, a series of 18.5 EGF-like repeats, 29 fibronectin type III repeats, and a carboxy-terminal fibrinogen-like domain. Because the structure of the protein encoded by the XB gene closely resembles tenascin, we term this protein tenascin-X (TN-X), and propose a simplified nomenclature system for the family of tenascins. RNase protection experiments show that the TN-X transcript is expressed ubiquitously in human fetal tissues, with the greatest expression in the fetal testis and in fetal skeletal, cardiac, and smooth muscle. Two adrenal-specific transcripts, P450c21B (steroid 21-hydroxylase) and Y (an untranslated transcript) overlap the XB gene on the complementary strand of DNA, yielding a unique array of overlapping transcripts: a "polygene." In situ hybridization histochemistry experiments show that the TN-X transcript and the P450c21 and Y transcripts encoded on the complementary DNA strand are all expressed in the same cells of the human adrenal cortex. Genetic data suggest that TN-X may be essential for life.

Adrenal Glands↗
PubMed1997

A rare type of overlapping genes in bacteriophage T4: gene 30.3' is completely embedded within gene 30.3 by one position downstream.

We have previously proposed the existence of one of the rarest types of overlapping genes in bacteriophage T4. We now present the results demonstrating that in a pair of T4 overlapping genes, 30.3 and 30.3', the smaller gene, 30.3', is entirely enclosed within the other by one position downstream. We have constructed plasmids in which different open reading frames from the gene 30.3 region were fused with the 5' end of the lacZ beta-galactosidase (betaGal) gene of Escherichia coli. The gene fusions have been obtained at the position of a HindIII site which was introduced just upstream from the stop codon of gene 30.3'. High betaGal activities have been estimated in the case of plasmids carrying 30.3::lacZ and 30.3'::lacZ fusions. The apparent molecular weights of the fusion proteins, the determined N-terminal sequences, as well as the detected betaGal activities, confirm the structure and arrangement of out-of-phase overlapping genes 30.3 and 30.3'.

Bacteriophage T4↗
PubMed1990

Translational efficiency of phi X174 lysis gene E is unaffected by upstream translation of the overlapping gene D reading frame.

The lysis gene E of bacteriophage phi X174 is entirely embedded in gene D. Expression studies of genes D and E in Escherichia coli minicells and lysis times obtained in the presence or absence of D translation showed that the simultaneous expression of gene D does not affect protein E production. Thus, unlike other overlapping gene pairs, gene E expression is independent from the upstream translation of gene D. lacZ fusion studies and primer extension inhibition analysis (toeprinting) revealed an intrinsically weak E ribosome-binding site, which seems to be the major factor determining the low expression rate of the gene and thus proper scheduling of cell lysis.

Amino Acid Sequence↗
PubMed2000

Lessons from sequenced genomes. Overlapping genes in Methanococcus jannaschii?

This paper describes our finding on overlapping genes in Methanococcus jannaschii genome. We found that one of the open reading frames (ORFs) within the M. jannaschii genome contains the nucleotide sequence of tRNA(Ser), which raises a serious question of the correctness of the initiation codon assignment for that ORF. We suggest that there are two other possible AUG initiation codons downstream from the TTG triplet, which was initially considered as a translation start site. Only one of the AUG triplets is preceded by the Shine-Dalgarno sequence that seems to be required for binding the ribosome and initiation of translation.

Amino Acid Sequence↗
PubMed2000

Genetic manipulation of equine arteritis virus using full-length cDNA clones: separation of overlapping genes and expression of a foreign epitope.

Equine arteritis virus (EAV) is an enveloped, positive-stranded RNA virus belonging to the family Arteriviridae of the order Nidovirales. The unsegmented, infectious genome of EAV is 12,704 nt in length [exclusive of the poly(A) tail] and contains eight overlapping genes that are expressed from a 3'-coterminal nested set of seven leader-containing mRNAs. To investigate the importance of the overlapping gene arrangement in the viral life-cycle and to facilitate the genetic manipulation of the viral genome, a series of mutant full-length cDNA clones was constructed in which either EAV open reading frames (ORFs) 4 and 5 or ORFs 5 and 6 or ORFs 4, 5, and 6 were separated by newly introduced AflII restriction endonuclease cleavage sites. RNA transcribed from each of these plasmids was infectious, demonstrating that the overlapping gene organization is not essential for EAV viability. Moreover, the recombinant viruses replicated with almost the same efficiency, i.e., reached nearly the same infectious titers as the wildtype virus, and stably maintained the mutations that were introduced. The AflII site engineered between ORFs 5 and 6 was subsequently used to generate a virus in which the ectodomain of the ORF 6-encoded M protein was extended with nine amino acids derived from the extreme N-terminus of the homologous protein of mouse hepatitis virus (MHV; family Coronaviridae, order Nidovirales). This nonapeptide contains a functional O-glycosylation signal as well as an epitope recognized by an MHV-specific monoclonal antibody, both of which were expressed by the recombinant virus. Although the hybrid virus had a clear growth disadvantage in comparison to the parental virus, three serial passages did not result in the loss of the foreign genetic material.

5' Untranslated Regions↗
PubMed1998

The rat androgen-binding protein (ABP/SHBG) gene contains triplet repeats similar to unstable triplets: evidence that the ABP/SHBG and the fragile X-related 2 genes overlap.

The rat androgen-binding protein/sex hormone-binding globulin (ABP/SHBG) gene is regulated by promoters P1 and PA. P1 regulates the mRNA encoding secreted ABP/SHBG, whereas PA regulates an alternate mRNA which encodes a modified protein that is targeted to the nucleus. Promoter PA is GC rich, consisting of 70-80% GC residues. During routine BLAST sequence analysis it was discovered that this GC-rich region is highly related to the human fragile X-related protein 2 (FXR-2) 5'-untranslated RNA sequence. Furthermore, the nucleotide coding sequence of the initial 14 FXR-2 amino acid residues was identical in the ABP/SHBG gene. The 5'-untranslated FXR-2 sequence contains triplet (CGG) repeats, which are also present in the rat ABP/SHBG gene. The meiotic instability of CGG repeats in the human fragile X (FMR1) gene causes the fragile X mental retardation syndrome. The data presented here suggest that the ABP/SHBG and FXR-2 genes overlap with each gene transcribed in the opposite direction. In support of this structure, the human ABP/SHBG and the FXR-2 genes map to the same site on chromosome 17. Thus, the ABP/SHBG gene contains triplet repeats in the alternate promoter PA. It will be of particular interest to determine if triplet instability affects ABP/SHBG gene expression. A triplet instability in the X-linked androgen receptor gene causes spinal and bulbar muscular atrophy.

Androgen-Binding Protein↗