Nonautonomous transposable elements in prokaryotes and eukaryotes

Hartl, Daniel L.; Lozovskaya, Elena R.; Lawrence, Jeffrey G.

doi:10.1007/bf00133710

Cited by 43 publications

(20 citation statements)

References 47 publications

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“…These data are consistent with a recent insertion of the IS5 transposon in this strain. Current models of transposon population dynamics are inconsistent with long-term stability of individual transposon insertions in prokaryotes (24,37,44).…”

Section: Discussionmentioning

confidence: 99%

The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli

Lawrence

Roth

1995

J Bacteriol

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The enteric bacterium Escherichia coli synthesizes cobalamin (coenzyme B 12 ) only when provided with the complex intermediate cobinamide. Three cobalamin biosynthetic genes have been cloned from Escherichia coli K-12, and their nucleotide sequences have been determined. The three genes form an operon (cob) under the control of several promoters and are induced by cobinamide, a precursor of cobalamin. The cob operon of E. coli comprises the cobU gene, encoding the bifunctional cobinamide kinase-guanylyltransferase; the cobS gene, encoding cobalamin synthetase; and the cobT gene, encoding dimethylbenzimidazole phosphoribosyltransferase. The physiological roles of these sequences were verified by the isolation of Tn10 insertion mutations in the cobS and cobT genes. All genes were named after their Salmonella typhimurium homologs and are located at the corresponding positions on the E. coli genetic map. Although the nucleotide sequences of the Salmonella cob genes and the E. coli cob genes are homologous, they are too divergent to have been derived from an operon present in their most recent common ancestor. On the basis of comparisons of G؉C content, codon usage bias, dinucleotide frequencies, and patterns of synonymous and nonsynonymous substitutions, we conclude that the cob operon was introduced into the Salmonella genome from an exogenous source. The cob operon of E. coli may be related to cobalamin synthetic genes now found among non-Salmonella enteric bacteria.Although commonly touted as one of the largest and oldest of the cofactors participating in modern biochemistry (20,23,59,60), the physiological importance of cobalamin (coenzyme B 12 ), especially among enteric bacteria, has remained enigmatic (58, 63). Cobalamin is derived from uroporphyrinogen III, a precursor in the synthesis of heme, siroheme, and chlorophylls as well as cobamides (Fig. 1). The conversion of uroporphyrinogen III to the complex intermediate cobinamide is referred to as part I of the biosynthetic pathway (hereafter designated CobI). Part II of the pathway (CobII) entails the biosynthesis of dimethylbenzimidazole (DMB) from probable flavin precursors (11,27,39). The covalent linkage of cobinamide, DMB, and a phosphoribosyl group donated by nicotinate mononucleotide is achieved by part III of the pathway (CobIII). Although most enteric bacteria can synthesize cobalamin de novo under either aerobic or anaerobic conditions (38), Escherichia coli synthesizes cobalamin only when provided with the complex intermediate cobinamide (38, 66); therefore, E. coli performs only parts II and III of the cobalamin biosynthetic pathway.The cobalamin biosynthetic genes in the closely related enteric bacterium Salmonella typhimurium have been characterized, and most constitute a large, 20-gene operon located at min 41 on the genetic map (28, 29, 52). It has been proposed that these genes are not ancestral to the Salmonella chromosome but have been introduced by horizontal transfer at or following the divergence of the salmonellae from Escherichia speci...

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Section: Discussionmentioning

confidence: 99%

The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli

Lawrence

Roth

1995

J Bacteriol

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Section: Population Dynamics Of Dna Transposons Within Genomes: the Mmentioning

confidence: 99%

“…The frequent emergence of nonautonomous derivatives coupled to the apparent lack of cispreference of eukaryotic transposases poses a major hurdle for the successful propagation of an autonomous element (70). Indeed, unless there exists a mechanism to prevent the formation of nonfunctional copies upon gap repair [see the possible case of Tam3 in snapdragon (198)], it can be predicted that autonomous copies will be rapidly out-numbered by nonautonomous copies (70,112). As copy number increases, the entire family potentially faces two constraints: (i) titration of the transposase by binding to multiple nonautonomous copies and (ii) an increased chance to trigger host-or self-induced repression mechanisms, such as RNA interference (RNAi) (1,69,112,173,177).…”

Section: Population Dynamics Of Dna Transposons Within Genomes: the Mmentioning

confidence: 99%

DNA Transposons and the Evolution of Eukaryotic Genomes

2007

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Transposable elements are mobile genetic units that exhibit broad diversity in their structure and transposition mechanisms. Transposable elements occupy a large fraction of many eukaryotic genomes and their movement and accumulation represent a major force shaping the genes and genomes of almost all organisms. This review focuses on DNA-mediated or class 2 transposons and emphasizes how this class of elements is distinguished from other types of mobile elements in terms of their structure, amplification dynamics, and genomic effect. We provide an up-to-date outlook on the diversity and taxonomic distribution of all major types of DNA transposons in eukaryotes, including Helitrons and Mavericks. We discuss some of the evolutionary forces that influence their maintenance and diversification in various genomic environments. Finally, we highlight how the distinctive biological features of DNA transposons have contributed to shape genome architecture and led to the emergence of genetic innovations in different eukaryotic lineages.

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“…It has been shown, how-ever, that genetic material integrated via LGT can constitute an entire gene (41,104), a partial (fragmentary) gene (10,49,75), or multiple (entire or fragmentary) adjacent genes, including multigene operons (34,48,81). We recently examined the transfer of genes and gene fragments among 144 prokaryote genomes (15,18), demonstrating that studies focusing entirely on whole-gene transfer are likely to underestimate the extent of LGT.…”

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confidence: 99%

Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements

2011

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The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13 Staphylococcus genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within S. aureus appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.Staphylococci are nonmotile but invasive Gram-positive bacteria that are associated with various pus-forming diseases in humans and other animals. The most prominent pathogenic species in the genus is Staphylococcus aureus, of which various strains colonize the nasal passages and skin in humans, causing illnesses that range from minor skin lesions or infections to life-threatening diseases, e.g., meningitis, septicemia (bacteremia), and toxic shock syndrome (55,67,94). The other species of Staphylococcus, although lacking genes that encode virulence factors and toxins, are opportunistic pathogens for immunocompromised patients (2, 74, 82).One of the major problems in the prognosis of staphylococcal infections is the progressive development of resistance in the Staphylococcus species to multiple antibiotics (14), e.g., methicillin (36, 102) and vancomycin (23, 84), which has, as in other pathogenic bacteria, been attributed to the susceptibility of the organisms to genetic transfer (22, 83). Lateral genetic transfer (LGT) occurs when the organisms acquire exogenous genetic material that encodes antibiotic resistance (6, 105), and this material becomes established in the lineage, whether by recombination into the genome or, potentially less stably, on an extrachromosomal genetic element (31, 86). In Staphylococcus, transfer of genetic material has been shown to be mediated by phage transduction and conjugative transfer (19,62,79).Although a number of studies have examined the frequency of LGT in prokaryotes us...

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Nonautonomous transposable elements in prokaryotes and eukaryotes

Cited by 43 publications

References 47 publications

The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli

The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli

DNA Transposons and the Evolution of Eukaryotic Genomes

Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements

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