<i>Neisseria gonorrhoeae</i>and humans perform an evolutionary LINE dance

Anderson, Mark T.; Seifert, H. Steven

doi:10.4161/mge.1.1.15868

Cited by 11 publications

(9 citation statements)

References 14 publications

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“…Notably, two isolates from 1980 and 2013, respectively, had a G70D mutation in a region of the L4 protein, encoded by rplD, associated with decreased susceptibility or resistance to macrolides, and both isolates were resistant to erythromycin but susceptible to azithromycin [18]. Finally, the first N. gonorrhoeae strain carrying parts of the human L1 element [25] was cultured already in this collection in 1946.…”

Section: Resultsmentioning

confidence: 99%

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): antimicrobial use/misuse selects for resistance and drives evolution

Golparian

Harris²,

Sánchez-Busó

et al. 2020

BMC Genomics

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Background: Multidrug-resistant Neisseria gonorrhoeae strains are prevalent, threatening gonorrhoea treatment globally, and understanding of emergence, evolution, and spread of antimicrobial resistance (AMR) in gonococci remains limited. We describe the genomic evolution of gonococci and their AMR, related to the introduction of antimicrobial therapies, examining isolates from 1928 (preantibiotic era) to 2013 in Denmark. This is, to our knowledge, the oldest gonococcal collection globally.Methods: Lyophilised isolates were revived and examined using Etest (18 antimicrobials) and whole-genome sequencing (WGS). Quality-assured genome sequences were obtained for 191 viable and 40 non-viable isolates and analysed with multiple phylogenomic approaches.Results: Gonococcal AMR, including an accumulation of multiple AMR determinants, started to emerge particularly in the 1950s-1970s. By the twenty-first century, resistance to most antimicrobials was common. Despite that some AMR determinants affect many physiological functions and fitness, AMR determinants were mainly selected by the use/misuse of gonorrhoea therapeutic antimicrobials. Most AMR developed in strains belonging to one multidrug-resistant (MDR) clade with close to three times higher genomic mutation rate. Modern N. gonorrhoeae was inferred to have emerged in the late-1500s and its genome became increasingly conserved over time.Conclusions: WGS of gonococci from 1928 to 2013 showed that no AMR determinants, except penB, were in detectable frequency before the introduction of gonorrhoea therapeutic antimicrobials. The modern gonococcus is substantially younger than previously hypothesized and has been evolving into a more clonal species, driven by the use/misuse of antimicrobials. The MDR gonococcal clade should be further investigated for early detection of strains with predispositions to develop and maintain MDR and for initiation of public health interventions.

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Section: Resultsmentioning

confidence: 99%

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): antimicrobial use/misuse selects for resistance and drives evolution

Golparian

Harris²,

Sánchez-Busó

et al. 2020

BMC Genomics

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“…However, horizontal transfer was reported for a minor fraction of LINE clades; these include transfer of jockey elements within Drosophila [46], Bov-B transfer from Squamata to the ancestor of Ruminantia [47, 48], insertion of additional C-terminal domain into ORF2 of insect R1 from plant viruses [49], and L1 transfer from humans to bacteria Neisseria gonorrhoeae [50]. Phylogenetic analysis made on the entire LINE ORF2 sequences, for which corresponding SINE partner is known [51], confirmed 11 clades reported by [45] and further enlarged the number of clades to 15 [51].…”

Section: Introductionmentioning

confidence: 99%

Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition

Grechishnikova

Poptsova

2016

BMC Genomics

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BackgroundIn the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3′UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA. However polyadenylation is a property of any messenger RNA, and how the LINE RT recognizes transposon and non-transposon RNAs remains an open question. It is likely that RNA secondary structures play an important role in RNA recognition by LINE encoded proteins.ResultsHere we selected a set of L1 and Alu elements from the human genome and investigated their sequences for the presence of position-specific stem-loop structures. We found highly conserved stem-loop positions at the 3′UTR. Comparative structural analyses of a human L1 3′UTR stem-loop showed a similarity to 3′UTR stem-loops of the stringent-type LINEs, which were experimentally shown to be recognized by LINE RT. The consensus stem-loop structure consists of 5–7 bp loop, 8–10 bp stem with a bulge at a distance of 4–6 bp from the loop. The results show that a stem loop with a bulge exists at the 3′-end of Alu. We also found conserved stem-loop positions at 5′UTR and at the end of ORF2 and discuss their possible role.ConclusionsHere we presented an evidence for the presence of a highly conserved 3′UTR stem-loop structure in L1 and Alu retrotransposons in the human genome. Both stem-loops show structural similarity to the stem-loops of the stringent-type LINEs experimentally confirmed as essential for retrotransposition. Here we hypothesize that both L1 and Alu RNA are recognized by L1 RT via the 3′-end RNA stem-loop structure. Other conserved stem-loop positions in L1 suggest their possible functions in protein-RNA interactions but to date no experimental evidence has been reported.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3344-4) contains supplementary material, which is available to authorized users.

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“…Anderson et al described horizontally transferred fragment of the human long interspersed nuclear element L1 to the genome of the strictly human pathogen Neisseria gonorhoeae. N. gonorhoeae transcripts contained L1 sequence, so L1-derived gene products may be produced [36,38].…”

Section: Discussionmentioning

confidence: 99%

“…The second possible mechanism of horiontal gene transfer is non-homologous end joining (NHEJ) recombination which could occure between fragmented copy of human gene and the recipient region of the bacterial genome. Although some bacterial species lack NHEJ machinery, alternative pathways of low frequency NHEJ have the potential to mediate horizontal gene transfer of exogenous sequences [38,40].…”

Section: Discussionmentioning

confidence: 99%

Intestinal flora of FAP patients containing APC-like sequences

Hainova¹,

Adamcikova²,

Ciernikova³

et al. 2014

neo

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Colorectal cancer mortality is one of the most common cause of cancer-related mortality. A multiple risk factors are associated with colorectal cancer, including hereditary, enviromental and inflammatory syndromes affecting the gastrointestinal tract. Familial adenomatous polyposis (FAP) is characterized by the emergence of hundreds to thousands of colorectal adenomatous polyps and FAP syndrome is caused by mutations within the adenomatous polyposis coli (APC) tumor suppressor gene. We analyzed 21 rectal bacterial subclones isolated from FAP patient 41-1 with confirmed 5bp ACAAA deletion within codons 1060-1063 for the presence of APC-like sequences in longest exon 15. The studied section was defined by primers 15Efor-15Erev, what correlates with mutation cluster region (MCR) in which the 75% of all APC germline mutations were detected. More than 90% homology was showed by sequencing and subsequent software comparison. The expression of APC-like sequences was demostrated by Western blot analysis using monoclonal and polyclonal antibodies against APC protein. To study missing link between the DNA analysis (PCR, DNA sequencing) and protein expresion experiments (Western blotting) we analyzed bacterial transcripts containing the 15Efor-15Erev sequence of APC gene by reverse transcription-PCR, what indicated that an APC gene derived fragment may be produced. We observed 97-100 % homology after computer comparison of cDNA PCR products. Our results suggest that presence of APC-like sequences in intestinal/rectal bacteria is enrichment of bacterial genetic information in which horizontal gene transfer between humans and microflora play an important role.

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Neisseria gonorrhoeaeand humans perform an evolutionary LINE dance

Cited by 11 publications

References 14 publications

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): antimicrobial use/misuse selects for resistance and drives evolution

Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): antimicrobial use/misuse selects for resistance and drives evolution

Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition

Intestinal flora of FAP patients containing APC-like sequences

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