Survey of multicopy single-stranded DNAs and reverse transcriptase genes among natural isolates of Myxococcus xanthus

An Unexplored Diversity of Reverse Transcriptases in Bacteria

Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.

Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens

Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.

Retrons, msDNA, and the bacterial genome

Retrons are distinct DNA sequences that code for a reverse transcriptase (RT) similar to the RTs produced by retroviruses and other types of retroelements. Retron DNAs are commonly associated with prophage DNA and are found in the genomes of a wide variety of different bacteria. The retron RT is used to synthesize a strange satellite DNA known as msDNA. msDNA is actually a complex of DNA, RNA, and probably protein. It is composed of a small, single-stranded DNA, linked to a small, single-stranded RNA molecule. The 5' end of the DNA molecule is joined to an internal guanosine residue of the RNA molecule by a unique 2'-5' phosphodiester bond. msDNA is produced in many hundreds of copies per cell, but its function remains unknown. Although retrons are absent from the genome of most members of a population of related bacteria, retrons may not be entirely benign DNAs. Evidence is beginning to suggest that retron elements may produce small but potentially significant effects on the host cell. This includes the generation of repeated copies of the msDNA sequence in the genome, and increasing the frequency of spontaneous mutations. Because these events involve the retron RT, this may represent a source of reverse transcription in the bacterial cell. Thus, the process of reverse transcription, a force that has profoundly affected the content and structure of most eukaryotic genomes, may likewise be responsible for changes in some prokaryotic genomes.

Retron reverse transcriptase rrtT is ubiquitous in strains of Salmonella enterica serovar Typhimurium

Bacterial retron reverse transcriptases are unusual enzymes which utilise the same RNA molecule as a template and also as a primer for initiation of the reverse transcription. Except for their relatively frequent presence in Myxococcus spp., they are considered as quite rare proteins. However, in this study we proved that retron reverse transcriptase is frequently found in certain serovars of Salmonella enterica. Using polymerase chain reaction (PCR), in strains of serovar Typhimurium, the rrtT (retron reverse transcriptase Typhimurium) gene was detected in 158 out of 175 tested field strains. On the other hand, in none of the 18 tested serovar Enteritidis strains the rrtT was detected in their genome. Detailed computer analysis allowed us to predict the sequence of msDNA and to propose that the final msDNA is free of any RNA. Furthermore, we predict that there are at least three different classes of retron reverse transcriptases.

The msDNAs of bacteria

msDNAs are small, structurally unique satellite DNAs found in a number of Gram-negative bacteria. Composed of hundreds of copies of single-stranded DNA--hence the name multicopy single-stranded DNA--msDNA is actually a complex of DNA, RNA, and probably protein. These peculiar molecules are synthesized by a reverse transcription mechanism catalyzed by a reverse transcriptase (RT) that is evolutionarily related to the polymerase found in the HIV virus. The genes, including the RT gene, responsible for the synthesis of msDNA are encoded in a retron, a genetic element that is carried on the bacterial chromosome. The retron is, in fact, the first such retroelement to be discovered in prokaryotic cells. This report is a comprehensive review of the many interesting questions raised by this unique DNA and the fascinating answers it has revealed. We have learned a great deal about the structure of msDNA: how it is synthesized, the structure and functions of the RT protein required to make it, its effects on the host cell, the retron element that encodes it, its possible origins and evolution, and even its potential usefulness as a practical genetic tool. Despite the impressive gains in our understanding of the msDNAs, however, the simple, fundamental question of its natural function remains an enduring mystery. Thus, we have much more to learn about the msDNAs of bacteria.

Low-molecular-weight plasmid of Salmonella enterica serovar Enteritidis codes for retron reverse transcriptase and influences phage resistance

Retron reverse transcriptases are unusual procaryotic enzymes capable of synthesis of low-molecular-weight DNA by reverse transcription. All of the so-far-described DNA species synthesized by retron reverse transcriptases have been identified as multicopy single-stranded DNA. We have shown that Salmonella enterica serovar Enteritidis is also capable of synthesis of the low-molecular-weight DNA by retron reverse transcriptase. Surprisingly, Salmonella serovar Enteritidis-produced low-molecular-weight DNA was shown to be a double-stranded DNA with single-stranded overhangs (sdsDNA). The sdsDNA was 72 nucleotides (nt) long, of which a 38-nt sequence was formed by double-stranded DNA with 19- and 15-nt single-stranded overhangs, respectively. Three open reading frames (ORFs), encoded by the 4,053-bp plasmid, were essential for the production of sdsDNA. These included an ORF with an unknown function, the retron reverse transcriptase, and an ORF encoding the cold shock protein homologue. This plasmid was also able to confer phage resistance onto the host cell by a mechanism which was independent of sdsDNA synthesis.

A mutational study of the site-specific cleavage of EC83, a multicopy single-stranded DNA (msDNA): nucleotides at the msDNA stem are important for its cleavage

Multicopy single-stranded DNA (msDNA) molecules consist of single-stranded DNA covalently linked to RNA. Such molecules are encoded by genetic elements called retrons. Unlike other retrons, retron EC83 isolated from Escherichia coli 161 produces RNA-free msDNA by site-specific cleavage of msDNA at 5'-TTGA/A-3', where the slash indicates the cleavage site. In order to investigate factors responsible for the msDNA cleavage, retron EC83 was treated with hydroxylamine and colonies were screened for cleavage-negative mutants. We isolated three mutants which were defective in msDNA cleavage and produced RNA-linked msDNA. They were all affected in msd, a gene for msDNA, with a base substitution at the bottom part of the msDNA stem. In contrast, base substitution at and around the cleavage site has no marked effect on msDNA synthesis or its cleavage. From these results, we concluded that the nucleotides at the bottom of the msDNA stem, but not the nucleotides at the cleavage site, play a major role in the recognition and cleavage of msDNA EC83.

Enhancement of frame-shift mutation by the overproduction of msDNA in Escherichia coli

A minor population of wild Escherichia coli strains contain retroelements called retrons, which produce a peculiar satellite DNA, multicopy single-stranded DNA (msDNA). It has been reported that mismatched base pairs in the secondary structure formed in msDNA are mutagenic in E. coli[Maas et al.(1994) Mol.Microbiol. 14,437-441; Maas et al. (1996) Mol. Microbiol, 19, 505-509]. We reexamined this proposal by converting mismatched base pairs to matched base pairs using a single msDNA species, msDNA-Ec86, or by deleting mismatched regions using msDNA-Ec73. We also examined the effect of reverse transcriptases (RT) without msDNA production on mutagenesis. All the constructs are under the lpp/lac promoter-operator control so that their mutagenic effects can be tested in the absence and the presence of a lac inducer. It was found that when the production of msDNA-Ec86 or Ec73 was induced, reversion frequencies from Lac- to Lac+ significantly increased in the case of a Lac- mutation caused by a frame-shift mutation, but much less by a substitution mutation. The removal of mismatched base pairs eliminated the high mutation frequencies, and the inducible expression of RT alone was not mutagenic. These results are consistent with the hypothesis of Maas and his associates that mismatched base pairs in msDNA sequester a cellular mismatch repair system, resulting in the increase of frame-shift mutations.

Starvation-induced expression of retron-Ec107 and the role of ppGpp in multicopy single-stranded DNA production

Multicopy single-stranded DNA is found as a small single-stranded RNA-DNA complex in certain wild-type strains of Escherichia coli as well as in other gram-negative bacteria. Using the promoter region of the previously characterized retron-Ec107 from E. coli ECOR70, I constructed a chromosomally located lacZ operon fusion. Examination of expression from the PEc107 promoter showed that activity increased sharply when cells entered stationary phase in rich medium or when they were starved for phosphate. The nucleotide guanosine-3',5'-bispyrophosphate was found to be a positive regulator of retron-Ec107 expression. Its presence is required for starvation-induced transcription of retron-Ec107 and multicopy single-stranded DNA production. It was also found that expression from the retron promoter is independent of the sigma factor sigmaS.

Structure, function, and evolution of bacterial reverse transcriptase

The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases. We first discuss a possible structure of bacterial reverse transcriptases on the basis of the known three-dimensional structure of HIV-1 reverse transcriptase, and how such a putative three-dimensional structure is able to recognize a single primer-template RNA molecule to initiate DNA chain elongation from the 2'-OH group of an internal G residue. This reaction leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded DNA) in which a single-stranded DNA branches out from an RNA molecule via a 2',5'-phosphodiester linkage. Second, the mobility of the bacterial retroelements called retrons, responsible for the production of msDNA, are discussed and compared with the mobility of group I and group II introns. Third, the original and evolution of bacterial reverse transcriptases are discussed in light of the question of whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases.

Bacterial reverse transcriptase and msDNA

Retrons are a new class of genetic elements found in the chromosome of a large number of different bacteria. These elements code for a reverse transcriptase (RT) that is structurally similar to the polymerases of retroviruses. The retron associated RT is responsible for the production of an unusual extrachromosomal satellite DNA, known as multicopy, single-stranded DNA (msDNA). Synthesis of msDNA is dependent on a novel self-priming mechanism, resulting in the formation of a 2',5'-phosphodiester bond. A comparison of bacterial RTs is presented, noting conserved and unique features of these polymerases. In addition, the origin, means of dissemination, and possible activities of these functionally obscure retroelements are discussed.

Phylogenetic comparison of retron elements among the myxobacteria: evidence for vertical inheritance

Twenty-eight myxobacterial strains, representing members from all three subgroups, were screened for the presence of retron elements, which are novel prokaryotic retroelements encoding reverse transcriptase. The presence of retrons was determined by assaying strains for a small satellite DNA produced by reverse transcription called multicopy, single-stranded DNA (msDNA). An msDNA-producing retron appeared to be absent from only one of the strains surveyed. DNA hybridization experiments revealed that retron elements similar to retron Mx162, first identified in Myxococcus xanthus, were found only among members of the Myxococcus subgroup; that is, each of the seven different genera which constitute this subgroup contained a Mx162 homolog. Another retron element also appeared to have a clustered distribution, being found exclusively within the Nannocystis subgroup of the myxobacteria. A retron element of the Mx162 type was cloned from Melittangium lichenicola, and its DNA sequence was compared with those of similar elements in M. xanthus and Stigmatella aurantiaca. Together, the degree of sequence diversity, the codon bias of the reverse transcriptase genes, and the clustered distribution of these retrons suggest a possible evolutionary scenario in which a common ancestor of the Myxococcus subgroup may have acquired this retroelement.

A physical map of the Myxococcus xanthus chromosome

A physical map of the 9.2-Mbp Myxococcus xanthus DK1622 chromosome at a resolution of 25 kbp was constructed by using a strategy that is applicable to virtually all microorganisms. Segments of the chromosome were used as hybridization probes to subdivide a yeast artificial chromosome (YAC) library into groups of linked clones. The clones were aligned by comparing their EcoRI restriction patterns. The groups of YAC clones ("contigs") were oriented and aligned with the genomic restriction map by means of common genetic and physical markers such as rare restriction sites and transposon insertions. Over 95% of the genome is represented by cloned DNA. Sixty genetic loci including > 100 genes, many of which play a role in fruiting body development, have been mapped in this way. Additional genes can now be located on the chromosome map by hybridization of their sequences to the ordered set of YAC chromosomes. The mapped genetic loci account for approximately 2% of the genome.

The retron: a bacterial retroelement required for the synthesis of msDNA

'Retrons' are bacterial retroelements responsible for the synthesis of msDNA, a hybrid nucleic acid consisting of a single-stranded DNA that is branched out from an internal guanosine of an RNA molecule via a 2',5'-phosphodiester linkage. Retrons are found in a minor population of various bacterial species and are extensively diverse. Two important questions now demanding attention are whether retrons are mobile elements and why are they so diverse?

Diversity of retron elements in a population of rhizobia and other gram-negative bacteria

Genetic elements called retrons reside on the chromosome of Escherichia coli and the myxobacteria and represent the first reverse transcriptase-encoding element to be found in a prokaryotic cell. All known retrons produce a functionally obscure RNA-DNA satellite molecule called multicopy single-stranded DNA (msDNA). We report here the presence of msDNA-producing retron elements in a number of new bacterial groups, including strains of the genera Proteus, Klebsiella, Salmonella, Nannocystis, Rhizobium, and Bradyrhizobium. Among a population of 63 rhizobia strains, only 16% contain a retron element. The rhizobia retrons appear to be heterogeneous in nucleotide sequence and show little similarity to previously studied retrons of E. coli and the myxobacteria.

111Indium labeling of microorganisms to facilitate the investigation of bacterial adhesion

The ability of bacteria to adhere to polymeric interfaces has attracted considerable attention in recent years. Metabolic labeling of microorganisms with 35S-methionine or other beta-emitters is commonly utilized for quantification of bacterial adhesion to biopolymers. Since the use of these isotopes is cumbersome, the possibility of labeling the microorganisms with 111Indium, a strong gamma-emitter, was explored. This report demonstrates that bacteria can be easily labeled with 111Indium. Staphylococcus aureus, Staphylococcus epidermiids, and Pseudomonas aeruginosa were labeled with either 111Indium-oxine or 35S-methionine; and labeling efficiency, retention of incorporated labels, and growth kinetics of labeled bacteria were compared under identical experimental conditions. Bacteria labeled with 111In-oxine incorporated approximately 90% of radioactivity within 10 min, whereas 35S-methionine incorporation required many hours of incubation. Both the incorporated isotopes were gradually released by rapidly growing bacteria into the suspension medium. Of the total incorporated labels, approximately 20% 111In and 15% 35S were released in the surrounding medium every 24 h. No release of incorporated labels occurred when cells were fixed with 2.5% buffered glutaraldehyde. Growth kinetics and scanning or transmission electron microscopic analysis showed no detectable differences among control (nonlabeled), 111In-, or 35S-labeled bacteria. Labeling of bacteria with 111In-oxine does not interfere with bacterial adherence. These observations suggest that 111In incorporation provides a simple and rapid method of labeling of microorganisms. Compared to currently available techniques, the use of 111In-labeled bacteria will facilitate the quantitation of adherent bacteria to interfaces.

Structure and biosynthesis of unbranched multicopy single-stranded DNA by reverse transcriptase in a clinical Escherichia coli isolate

It has been shown that retrons, retro-elements in bacteria, produce a reverse transcriptase (RT) and multicopy single-stranded DNA (msDNA) whose 5' end is covalently linked to RNA (msdRNA) by a 2'-5' phosphodiester bond. Here, I show that a retron in clinical Escherichia coli strain 161 produces an msDNA unlinked to RNA. The msDNA produced by this retron is a 79-nucleotide-long single-stranded DNA with monophosphate on its 5' terminus. When the retron in strain 161 is cloned into E. coli K-12, the majority of msDNA produced in the clone is the same as the msDNA in the clinical strain. However, in the K-12 clone, about 10% of the msDNA produced is present as a DNA covalently linked to RNA. The DNA part of this RNA-DNA compound is an 83 nucleotides long with the same sequence as the unbranched msDNA, except for the presence of four additional nucleotides at the 5' side. From the analysis of the RNA-DNA compound and the results of in vitro synthesis, I show that the primary product of reverse transcription in this retron is an 83-nucleotide-long DNA covalently linked to RNA. This RNA-DNA compound is further processed to the final product, the 79-nucleotide-long msDNA with a terminal 5' monophosphate, by an endonucleolytic cleavage between the fourth and fifth positions of the DNA component of the RNA-DNA compound. The minimum region required for the production of such msDNA free of RNA contains only genes known to be required for the synthesis of branched msDNA-RNA compound in other retrons (msd, msr and ret). This suggests that either the RT has an endonuclease activity or that the msDNA-RNA compound is autocatalytically processed.

Similarity between the Myxococcus xanthus and Stigmatella aurantiaca reverse transcriptase genes associated with multicopy, single-stranded DNA

To determine the evolutional relationship of bacterial retroelements of Myxococcus xanthus and Stigmatella aurantiaca, the nucleotide sequence of 3,060 bases encompassing msr, msd, and the upstream region of msd (downstream of msr) of S. aurantiaca DW4 was determined and compared with the same region from M. xanthus. An open reading frame was found 92 bases upstream of msd which encoded a polypeptide of 480 amino acid residues having 73% identity with the reverse transcriptase of M. xanthus. Together with high homologies in msr (86%) and msd (81%) regions, the present data indicate that the reverse transcriptase genes as well as the retrons of M. xanthus (retron-Mx162) and S. aurantiaca (retron-Sa163) were derived from a common progenitor retron which possibly before the two myxobacterial species diverged.

Retron-Ec107 is inserted into the Escherichia coli genome by replacing a palindromic 34bp intergenic sequence

Some natural isolates of Escherichia coli have been shown to produce a unique branched RNA-linked single-stranded DNA called msDNA. These bacteria contain a retro-element called retron consisting of the msr-msd region and the gene for reverse transcriptase (RT). All three E. coli retrons characterized to date have been shown to be integrated into a prophage or to be associated with phage-related genes. In this report, we identified a new msDNA from an E. coli wild strain. Using the msDNA as a probe, the retron for the msDNA was cloned and its DNA sequence was determined. The retron was found to consist of a 1.3kb DNA fragment, making it the smallest retron isolated to date. The msDNA produced from the retron consists of a 107 base single-stranded DNA, which is considered to be branched out from the 18th G residue of a 75-base RNA molecule by a 2',5'-phosphodiester linkage. Thus, the msDNA and the retron were designated msDNA-Ec107 and retron-Ec107, respectively. Most significantly, retron-Ec107 was inserted into the E. coli genome by replacing a 34bp intergenic sequence between the pyrE and ttk genes located at 82 min on the E. coli chromosome. Interestingly, the retron contains palindromic structures at both ends and the E. coli 34bp intergenic sequence also contains a 10bp inverted repeat structure. These palindromic structures might have played a role in the integration of retron-Ec107 into the E. coli genome.