Intragenic regulation of the synthesis of phi chi 174 gene A proteins

Overlapping genes in natural and engineered genomes

Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.

Agrobacterium tumefaciens and A. rhizogenes use different proteins to transport bacterial DNA into the plant cell nucleus

Agrobacterium tumefaciens and A. rhizogenes transport single‐stranded DNA (ssDNA; T‐strands) and virulence proteins into plant cells through a type IV secretion system. DNA transfer initiates when VirD2 nicks border sequences in the tumour‐inducing plasmid, attaches to the 5′ end, and pilots T‐strands into plant cells. Agrobacterium tumefaciens translocates ssDNA‐binding protein VirE2 into plant cells where it targets T‐strands into the nucleus. Some A. rhizogenes strains lack VirE2 but transfer T‐strands efficiently due to the GALLS gene, which complements an A. tumefaciens virE2 mutant. VirE2 and full‐length GALLS (GALLS‐FL) contain nuclear localization sequences that target these proteins to the plant cell nucleus. VirE2 binds cooperatively to T‐strands allowing it to move ssDNA without ATP hydrolysis. Unlike VirE2, GALLS‐FL contains ATP‐binding and helicase motifs similar to those in TraA, a strand transferase involved in conjugation. VirE2 may accumulate in the nucleus and pull T‐strands into the nucleus using the force generated by cooperative DNA binding. GALLS‐FL accumulates inside the nucleus where its predicted ATP‐dependent strand transferase may pull T‐strands into the nucleus. These different mechanisms for nuclear import of T‐strands may affect the efficiency and quality of transgenic events in plant biotechnology applications.

The Agrobacterium rhizogenes GALLS gene encodes two secreted proteins required for genetic transformation of plants

Agrobacterium tumefaciens and Agrobacterium rhizogenes are related pathogens that cause crown gall and hairy root diseases, which result from integration and expression of bacterial genes in the plant genome. Single-stranded DNA (T strands) and virulence proteins are translocated into plant cells by a type IV secretion system. VirD2 nicks a specific DNA sequence, attaches to the 5' end, and pilots the DNA into plant cells. A. tumefaciens translocates single-stranded DNA-binding protein VirE2 into plant cells where it likely binds T strands and may aid in targeting them into the nucleus. Although some A. rhizogenes strains lack VirE2, they transfer T strands efficiently due to the GALLS gene, which complements an A. tumefaciens virE2 mutant for tumor formation. Unlike VirE2, full-length GALLS (GALLS-FL) contains ATP-binding and helicase motifs similar to those in TraA, a strand transferase involved in conjugation. GALLS-FL and VirE2 contain nuclear localization signals (NLS) and secretion signals. Mutations in any of these domains abolish the ability of the GALLS gene to substitute for virE2. Here, we show that the GALLS gene encodes two proteins from one open reading frame: GALLS-FL and a protein comprised of the C-terminal domain, which initiates at an internal in-frame start codon. On some hosts, both GALLS proteins were required to substitute for VirE2. GALLS-FL tagged with yellow fluorescent protein localized to the nucleus of tobacco cells in an NLS-dependent manner. In plant cells, the GALLS proteins interacted with themselves, VirD2, and each other. VirD2 interacted with GALLS-FL and localized inside the nucleus, where its predicted helicase activity may pull T strands into the nucleus.

mRNA stabilizing signals encoded in the genome of the bacteriophage phi x174

In Escherichia coli cells infected with bacteriophage phi x174, mRNAs initiated by promoters PB and PD terminate after genes J, F, G, or H (TJ, TF, TG, or TH). These RNAs are relatively stable and contain mRNA-stabilizing signals at their 3' ends. These signals were cloned after gene D of phi x174 in an expression vector plasmid. The cloned signals stabilize mRNA of the upstream gene D and the stabilized mRNA is translationally functional. When these signals are inserted in reverse, no stabilizing effect on mRNA is observed indicating that the correct sequences at the 3' ends of transcripts determine their stability. When a stabilizing signal (+) and a mutated stabilizing signal (-) which has reduced stabilizing activity are tandemly inserted after gene D, two sets of 3' termini of the transcript are observed indicating that both signals also function as terminators. The amount of gpD synthesized from these constructs varies depending upon the relative positions of the (+) or (-) signals after gene D. The stabilizing function seems to act by preventing mRNA degradation from the 3' to 5' direction. Several common features of these stabilizers are described.

Mechanism of replication of bacteriophage phi X174. XXII. Site-specific mutagenesis of the A* gene reveals that A* protein is not essential for phi X174 DNA replication

The A and A* proteins of phage phi X174 are encoded in the same reading frame in the viral genome; the smaller A protein is the result of a translational start signal with the A gene. To differentiate their respective functions, oligonucleotide-directed site-specific mutagenesis was used to change the ATG start codon of the phi X 174 A* gene, previously cloned into pCQV2 under lambda repressor control, into a TAG stop codon. The altered A gene was then inserted back into phi X replicative form DNA to produce an amber mutant, phi XamA*. Two different Escherichia coli amber suppressor strains infected with this mutant produced viable progeny phage with only a slight reduction in yield. In Su+ cells infected with phi XamA*, phi X gene A protein, altered at one amino acid, was synthesized at normal levels; A* protein was not detectable. These observations indicate that the A* protein increases the replicative efficiency of the phage, perhaps by shutting down host DNA replication, but is not required for replication of phi X174 DNA or the packaging of the viral strand under the conditions tested.

Developmental expression of three proteins from the first gene of the RNA polymerase sigma 43 operon of Bacillus subtilis

The first gene of the Bacillus subtilis RNA polymerase sigma 43 operon, P23, has a protein-coding capacity of 23,000 daltons. Sequence analysis revealed three potential translational initiation sites within the same reading frame, which could encode proteins of 23,000 (P23), 19,000 (P19), and 9,000 (P9) daltons, respectively. An internal promoter (P3), which is expressed only during the sporulation stage, is located between the second and the third translational start sites. By protein fusion to the Escherichia coli beta-galactosidase gene, we showed that all three translational initiation sites of the P23 gene are used in vivo in both E. coli and B. subtilis, and regulation for differential expression of the three proteins during the development of B. subtilis is coupled to the transcriptional promoter switching mechanism. The physiological function of these multiple gene products is unknown and is currently under investigation.

Revised genetic map of the distal end of the F transfer operon: implications for DNA helicase I, nicking at oriT, and conjugal DNA transport

The DNA transfer stage of conjugation requires the products of the F sex factor genes traMYDIZ and the cis-acting site oriT. Previous interpretation of genetic and protein analyses suggested that traD, traI, and traZ mapped as contiguous genes at the distal end of the transfer operon and saturated this portion of the F transfer region (which ends with an IS3 element). Using antibodies prepared against the purified TraD and TraI proteins, we analyzed the products encoded by a collection of chimeric plasmids constructed with various segments of traDIZ DNA. We found the traI gene to be located 1 kilobase to the right of the position suggested on previous maps. This creates an unsaturated space between traD and traI where unidentified tra genes may be located and leaves insufficient space between traI and IS3 for coding the 94-kilodalton protein previously thought to be the product of traZ. We found that the 94-kilodalton protein arose from a translational restart and corresponds to the carboxy terminus of traI; we named it TraI*. The precise physical location of the traZ gene and the identity of its product are unknown. The oriT nicking activity known as TraZ may stem from unassigned regions between traD and traI and between traI and IS3, but a more interesting possibility is that it is actually a function of traI. On our revised map, the position of a previously detected RNA polymerase-binding site corresponds to a site at the amino terminus of traI rather than a location 1 kilobase into the coding region of the gene. Furthermore, the physical and genetic comparison of the F traD and traI genes with those of the closely related F-like conjugative plasmids R1 and R100 is greatly simplified. The translational organization we found for traI, together with its identity as the structural gene for DNA helicase I, suggests a possible functional link to several other genes from which translational restart polypeptides are expressed. These include the primases of the conjugative plasmids ColI and R16, the primase-helicase of bacteriophage T7, and the cisA product (nickase) of phage phi X174.

Expression of the cloned bacteriophage phi X174 A* gene in Escherichia coli inhibits DNA replication and cell division

The A* gene of bacteriophage phi X174 has been cloned into the inducible expression vector pCQV2 under conditions allowing its lethal action to be controlled by the lambda cI857 repressor. Upon induction of expression, DNA synthesis in Escherichia coli carrying the recombinant plasmid is severely inhibited; however, these same cells permit beta-galactosidase induction at a rate similar to that observed in control cells at the inducing (for A*) temperature. Cells in which A* is expressed form filaments and produce more RecA protein, indicating at least a partial induction of the SOS response; however, there is no evidence of damage to the bacterial chromosome. It appears that the A* protein has as one function the inhibition of cell division and DNA replication but not transcription or protein synthesis during phage infection.

Role for the J-F intercistronic region of bacteriophages phi X174 and G4 in stability of mRNA

A hairpin-like secondary structure in the intercistronic region between genes J and F of bacteriophages, phi X174 and G4 has been postulated to act as a transcription termination signal. We analyzed the in vivo transcripts of both phages and mutants derived from them with modifications of this hairpin structure. The phi X174 mutants appeared to fall into two groups with respect to the stability of two mRNA species. Class 1 mutants showed an mRNA profile very similar to the parental strain, whereas class 2 mutants lacked two major mRNA species normally terminated near the J-F region. The G4 mutants behaved like class 2 mutants of phi X174. Analysis of the stability of phi X174 mRNA revealed that messages specific for the genes upstream of the hairpin turn over more rapidly in class 2 mutants than in class 1 mutants. In class 1 mutants, the mRNA decay rates are similar but not identical to those of the wild-type strain. These data suggest a role for the nucleotide sequence within the J-F intercistronic region in mRNA degradation. They further imply that transcription termination occurs downstream from this site.

The interaction of the A and A* proteins of bacteriophage phi X174 with single-stranded and double-stranded phi X DNA in vitro

The binding of the bacteriophage phi X 174-coded A and A* proteins to single-stranded (ssDNA) and double-stranded (dsDNA ) phi X DNA was studied by electron microscopy. The interaction of the A* protein with ssDNA and dsDNA was also studied by sedimentation velocity centrifugation. It was shown that the binding of the A and A* proteins to ssDNA occurs in a non-cooperative manner and requires no or very little sequence specificity under the conditions used here. Both protein-ssDNA complexes have the same compact structure caused by intrastrand cross-linking through the interaction of protein molecules with separate parts of the ssDNA molecule. The A protein does not bind to phi X dsDNA in the absence of divalent cations. The A* protein does bind to dsDNA, although it has a strong preference for binding to ssDNA. The structure of the A* protein-dsDNA complexes is different from that of the A* protein-ssDNA complexes, as the former have a rosette-like structure caused by protein-protein interactions. High ionic strengths favour the formation of large condensed aggregates.

Overlap between ampC and frd operons on the Escherichia coli chromosome

The promoter for the Escherichia coli ampC beta-lactamase gene is shown to be located within the last gene of the fumarate reductase (frd) operon. Evidence is presented that the ampC attenuator serves as the terminator for transcription of this preceding operon. The nucleotide sequence was determined for two proteins that were shown to be encoded by a DNA segment preceding the ampC gene. The two proteins consisted of 131 and 119 triplets and had molecular weights of 15,000 and 13,100, respectively. The twelve COOH-terminal amino acids of the 13,100 molecular weight protein were found to overlap the ampC promoter. Accordingly, a G.C insertion in the promoter gave both increased transcription of ampC and a frameshift in this overlapping gene, resulting in readthrough proteins. Thus, we describe a type of very compact genetic organization of operons in prokaryotes.

The mechanism of replication of phi X 174. XVIII. Gene A and A* proteins of phi X 174 bind tightly to phi X 174 replicative form DNA

Evidence is presented that the gene A and A * proteins of bacteriophage phi X 174 form covalent associations with the 5' ends of the DNA molecules when superhelical phi X replicative form DNA is nicked by a combination of these proteins in vitro. This evidence is: 1, The 5' ends of the DNA molecules nicked by the gene A protein and reacted with bacterial alkaline phosphatase were protected against subsequent phosphorylation by polynucleotide kinase even after treatment of the nicked DNA with SDS and pronase followed by centrifugation on a high-salt neutral sucrose gradient. 2, Iodinated pronase-sensitive material remained attached to the nicked replicative form DNA and could not be removed by exposure to SDS or 2 M NaCl, either by sedimentation through high-salt neutral sucrose gradients, or by CsCl equilibrium centrifugation. 3, Iodinated pronase-sensitive material was detected on DNA that had been nicked during the reaction, but not on unreacted DNA. 4, Electrophoresis of the iodinated pronase-sensitive, DNA-bound material in SDS-polyacrylamide gels after DNAse digestion revealed that it was composed almost entirely polypeptides with electrophoretic mobilities similar to those of the gene A and A * proteins. We speculate that the gene * protein may be essential for normal progeny single-stranded DNA synthesis in vivo.

Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code

Strong rhythms with a period of three bases have been seen while correlating the relative positions of purines and pyrimidines and of the four individual bases in the complete DNA sequence of the viruses phi X174, G4 and fd. Generally weaker variations of the same type have been found in the DNA virus SV40, the plasmid pBR322, the RNA virus MS2, and elsewhere in procaryotes and eucaryotes (e.g. in a ribosomal protein gene cluster of E. coli and the sea urchin histone genes). From the interrelation of four-base with purine-pyrimidine rhythms it seems that the purine-pyrimidine relationships have a basic significance. An explanation is proposed in terms of the former use of a comma-less genetic code (i.e. readable only in one frame) of the general form RNY (R = purine, Y = pyrimidine and N = purine or pyrimidine). In spite of subsequent mutation, there appears to be still enough of the primitive messages remaining to produce these periodic variations with their characteristic properties in phase and amplitude. Particularly good evidence for this hypothesis is provided by the fact that the phases for the stronger rhythms are the same in all the genomes tested and can be successfully predicted by a simple consideration of the original RNY pattern. With regard to amplitude it can be similarly foreseen which variations will be more clearly marked than others. The observed behaviour of the amplitude as the separation between correlated bases increases is also explained by the insertions, deletions and point mutations which have occurred. Additionally it is possible to account for some notable features of the non-random use of codons for the same amino acid by this theory.

Stability of bacteriophage phi X174-specific mRNA in vivo

Different-size species of phi X174-specific mRNA's decayed exponentially, with half-lives ranging from 4.5 to 11 min.

Recognition of two initiation codons for the synthesis of phage fd gene 2 protein

Bacteriophage fd gene 2 protein was specifically labeled with radioactive amino acids and was isolated from membranous cell structures as an apparently homogenous protein. Amino acid sequence analysis revealed that the protein was initiated at two distinct AUG codons close to the ribosome binding site. The two resulting translation products were found to begin with a deformylated methionine residue. Initiation at the first signal was used for 90% of the chains and at the second signal for 10% of the sequenced molecules. The use of one or the other chain start may influence functions of gene 2 protein.

Overlapping genes at the cheA locus of Escherichia coli

The cheA locus of Escherichia coli, which is required for chemotactic behavior, encodes two polypeptide products designated p[cheA]L and p[cheA]S. The mode of synthesis of these two proteins was investigated by transferring various missense and nonsense mutations to a lambda transducing phage and observing the mutant cheA products made after infection of ultraviolet-irradiated host cells. Missense mutations had no effect on either the size or the relative amounts of the two cheA polypeptides. Most nonsense mutations caused premature translational termination of both cheA products, indicating that p[cheA]L and p[cheA]S must be translated from the same coding sequence in the same reading frame. Two exceptional nonsense alleles at the promoter-proximal end of cheA made an intact p[cheA]s but no detectable p[cheA]L. These findings show that the cheA locus may contain two different sites for initiation of translation. The synthesis of both proteins can be effected by the same promoter, but it is not yet clear whether both are translated from identical mRNA molecules. Complementation studies of cheA mutants provided evidence for two functional activities, one associated with the amino terminus of p[cheA]L and the other with the common portions of p[cheA]L and p[cheA]S. It is possible that each cheA product has a different function required for chemotaxis. The possible roles of these two products and the functional significance of bacterial genes with overlapping coding sequences are discussed.

Morphogenetic genes C and Nu3 overlap in bacteriophage lambda

In bacteriophage lambda, genes C and Nu3, two of the four cistrons which are essential for normal prohead formation, have overlapping nucleotide sequences. These genes are translated in the same reading frame so that the Nu3 protein is identical to the COOH-terminal one-third of the C protein. This structural relationship may provide for the functional interaction of the C and Nu3 proteins through their regions of structural homology during prohead assembly. The in-phase overlapping organisation of genes may constitute a general strategy to facilitate the mutual interaction of a pair of proteins through their common structural domains.

Analysis of in vitro replication of different DNAs

The conversion of single-stranded circular DNA to duplex DNA in vitro occurs by at least three different mechanisms. These differences reside in the manner of priming of these DNAs. In contrast, the elongation of primed DNA templates is a general reaction. A number of these proteins have been isolated and further characterized. In addition, cell-free preparations capable of supporting phi X RFI DNA replication as well as the synthesis of progeny viral phi X174 single-stranded circular DNA have been prepared.

Nucleotide sequence of bacteriophage G4 DNA

The 5,577 nucleotide long sequence of bacteriophage G4 DNA has been determined using the 'plus and minus' and chain termination methods of DNA sequencing. This sequence has been compared with that of the closely related bacteriophage phiX174 (refs 1, 55). In the coding regions there is an average of 33.1% nucleotide sequence differences between the two genomes, but the distribution of these changes is not random and the sequence of some genes is more conserved than others. There is less sequence similarity between the untranslated intergenic regions of G4 and phiX174, but despite this the sequences of the J/F, F/G and H/A untranslated spaces in both genomes have similar sized hairpin loops, which may be related to their function.

Nucleotide sequence of bacteriophage phi X174 DNA

A DNA sequence for the genome of bacteriophage phi X174 of approximately 5,375 nucleotides has been determined using the rapid and simple 'plus and minus' method. The sequence identifies many of the features responsible for the production of the proteins of the nine known genes of the organism, including initiation and termination sites for the proteins and RNAs. Two pairs of genes are coded by the same region of DNA using different reading frames.

DNA sequence of a region of the phi X174 genome coding for a ribosome binding site

The DNA region corresponding to a newly identified ribosome binding site in phi X174 DNA is sequenced and mapped in relation to the physical map of phi X174. Assignments of the binding site to a specific gene are discussed, and the possibility of a second case of overlapping genes in phi X174 is considered.

Mapping of in vivo messenger RNAs for bacteriophage phiX-174

In vivo messenger RNA for bacteriophage phiX174 was fractionated in agarose gels into a number of discrete species ranging in size from 0.23 X 10(6) to 2.3 X 10(6) daltons. These RNA species were eluted from the gels and hybridized to specific fragments derived from phiX-174 replicative form DNA by cleavage with restriction enzymes. A map of the orientation of in vivo messenger RNAs with respect to the bacteriophage genetic map was constructed. This map indicated that initiation of messenger RNA occurred before gene B, gene C or D, and probably before gene A and that termination occurred after genes E, F, G, and H. Termination of transcription at any particular site appeared not to be entirely effective such that a number of overlapping transcripts with the same 5'-terminus was observed. Messenger RNA for gene A seemed to be relatively unstable.

Recognition properties of the beta subunit of Escherichia coli ribonucleic acid polymerase

Changes in the phage protein patterns obtained by gel electrophoresis of extracts from phage S13 and phiX174 infection of rifampin-resistant hosts suggest that the beta subunit of ribonucleic acid polymerase of Escherichia coli has a function in the recognition of promoter or terminator sites or both. The altered protein patterns also provide information on the location of some ribonucleic acid polymerase recognition signals in S13 deoxyribonucleic acid. There is a promoter site before gene A, which lies either in gene H or between H and A. There is evidence for a promotor between genes C and D or in gene C. There is either a terminator or a promoter somewhere between the end of gene D and the beginning of gene F.

Restriction-enzyme-cleavage maps of bacteriophage M13. Existence of an intergenic region on the M13 genome

Replicative form DNA of bacteriophage M13 was cleaved into specific fragments by an endonuclease isolated from Hemophilus aegyptius (endoR.HaeII) and an endonuclease from Arthrobacter luteus (endoR.AluI). The fragments were ordered as to construct a circular map of the phage M13 genome by: (a) using each fragment as a primer for the synthesis in vitro of its respective neighbour and (b) digesting the isolated fragments with the Hemophilus aegyptius enzyme endoR.HaeII or the Hemophilus aphirophilus enzyme endoR.HapII and subsequent analysis of the overlapping sets of fragments. The resulting physical map was correlated with the M13 genetic map by marker rescue experiments with amber mutant phage DNAs and purified wild-type fragments. From the results of these analyses it has been concluded that gene II and gene V are contiguous on the genetic map. Evidence is provided that there is an internal start of RNA synthesis within the C-terminal region of gene II which then ultimately leads to the synthesis of X protein. Furthermore, we conclude that there is an intergenic space of considerable length (450-500 base pairs) which is located between gene II and gene IV on the M13 genome. The function of this intergenic region as the origin site for phage DNA replication is discussed.

Gene A product of phi X174 is required for site-specific endonucleolytic cleavage during single-stranded DNA synthesis in vivo

A functional gene A product of phi X174 was found to be required at the stage of single-stranded DNA synthesis. A precursor complex that synthesizes single-stranded DNA (50S complex [Fujisawa and Hayashi, 1976]) was isolated from cells infected with wild-type or with temperature-sensitive gene A mutant phage. Proper cleavage of the single-stranded viral DNA did not occur in cells infected with the temperature-sensitive gene A mutant under restrictive conditions. This resulted in (i) accumulation of linear viral DNA molecules of 2 units in length in the 50S complex and (ii) cessation of elongation of viral-strand DNA after one complete cycle of single-stranded DNA synthesis.

Viral DNA-synthesizing intermediate complex isolated during assembly of bacteriophage phi X174

A DNA protein complex that is a precursor of mature phi X174 phage was isolated. The complex sedimented with an S value of 50 in a sucrose gradient and contained phage DNA consisting of a replicative form molecule with an extended tail of single-stranded viral DNA. The viral-strand DNA ranged from one to two genomes in length. Proteins coded on the phi X174 genome as well as the host genome were associated with the viral DNA in the 50S precursor complex. Our results indicated that both viral DNA synthesis and cleavage of the growing viral-strand DNA occurred in the 50S complex.