Articoli di riviste: "MOBT relaxase"

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Libante, Virginie, Nazim Sarica, Abbas Mohamad Ali, Chloé Gapp, Anissa Oussalah, Gérard Guédon, Nathalie Leblond-Bourget e Sophie Payot. "Mobilization of IMEs Integrated in the oriT of ICEs Involves Their Own Relaxase Belonging to the Rep-Trans Family of Proteins". Genes 11, n. 9 (26 agosto 2020): 1004. http://dx.doi.org/10.3390/genes11091004.

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Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide–streptogramin A–pleuromutilin resistance among Firmicutes.

2

Pluta, Radoslaw, D. Roeland Boer, Fabián Lorenzo-Díaz, Silvia Russi, Hansel Gómez, Cris Fernández-López, Rosa Pérez-Luque, Modesto Orozco, Manuel Espinosa e Miquel Coll. "Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance". Proceedings of the National Academy of Sciences 114, n. 32 (24 luglio 2017): E6526—E6535. http://dx.doi.org/10.1073/pnas.1702971114.

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Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOBV family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOBV relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterized histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. We discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOBV histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.

3

Meyer, Richard. "Mapping Type IV Secretion Signals on the Primase Encoded by the Broad-Host-Range Plasmid R1162 (RSF1010)". Journal of Bacteriology 197, n. 20 (3 agosto 2015): 3245–54. http://dx.doi.org/10.1128/jb.00443-15.

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ABSTRACTThe plasmid R1162 (RSF1010) encodes a primase essential for its replication. This primase makes up the C-terminal part of MobA, a multifunctional protein with the relaxase as a separate N-terminal domain. The primase is also translated separately as the protein RepB′. Here, we map two signals for type IV secretion onto the recently solved structure of RepB′. One signal is located internally within RepB′ and consists of a long α-helix and an adjacent disordered region rich in arginines. The second signal is made up of the same α-helix and a second, arginine-rich region at the C-terminal end of the protein. Successive arginine-to-alanine substitutions revealed that either signal can be utilized by the type IV secretion complex of the plasmid R751. The internal signal also enables conjugal transfer when linked to the relaxase part of MobA. Both signals are similar to those previously identified for type IV secretion substrates in the Vir system ofAgrobacterium tumefaciens. Moreover, the C-terminal arginine-rich segment of RepB′ has been shown to be secreted by Vir. However, with R751, the signals require MobB, an R1162-encoded accessory protein active in conjugal transfer. The results of two-hybrid assays revealed that MobB interacts, via its membrane-associated domain, with the R751 plasmid coupling protein TraG. In addition, MobB interacts with a region of MobA just outside the RepB′ domain. Therefore, MobB is likely an adaptor that is essential for recognition of the primase-associated signals by the R751 secretion machinery.IMPORTANCEFor most plasmids, type IV secretion is an intrinsic part of the mechanism for conjugal transfer. Protein relaxases, bound to the 5′ end of the transferring strand, are mobilized into recipient cells by the type IV pathway. In this work, we identify and characterize two signals for secretion in the primase domain of MobA, the relaxase of the IncQ plasmid R1162 (RSF1010). We also show that the adaptor protein MobB is required for engagement of these signals with the R751 coupling protein TraG. These results clarify the location and properties of secretion signals active during the conjugal transfer of plasmid DNA.

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Heilers, Jan-Hendrik, Jens Reiners, Eva-Maria Heller, Annika Golzer, Sander H. J. Smits e Chris van der Does. "DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island". Nucleic Acids Research 47, n. 15 (5 luglio 2019): 8136–53. http://dx.doi.org/10.1093/nar/gkz577.

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Abstract Relaxases of the MOBH family are often found on large plasmids, genetic islands and integrative conjugative elements. Many members of this family contain an N-terminal relaxase domain (TraI_2) followed by a disordered middle part and a C-terminal domain of unknown function (TraI_2_C). The TraI_2 domain contains two putative metal-binding motifs, an HD domain motif and an alternative 3H motif. TraI, encoded within the gonococcal genetic island of Neisseria gonorrhoeae, is the prototype of the MOBH family. SAXS experiments showed that TraI_2 and TraI_2_C form globular structures separated by an extended middle domain. The TraI_2 domain cleaves oriT-ssDNA in a site-specific Mn2+ or Co2+ dependent manner. The minimal oriT encompasses 50 nucleotides, requires an inverted repeat 3′ of the nic-site and several nucleotides around nic for efficient cleavage. Surprisingly, no stable covalent relaxase-DNA intermediate was observed. Mutagenesis of conserved tyrosines showed that cleavage was abolished in the Y212A mutant, whereas the Y212F and Y212H mutants retained residual activity. The HD and the alternative 3H motifs were essential for cleavage and the HD domain residues D162 and D267 for metal ion binding. We propose that the active site binds two metal ions, one in a high-affinity and one in a low-affinity site.

5

Tsvetkova, Krassimira, Jean-Christophe Marvaud e Thierry Lambert. "Analysis of the Mobilization Functions of the Vancomycin Resistance Transposon Tn1549, a Member of a New Family of Conjugative Elements". Journal of Bacteriology 192, n. 3 (4 dicembre 2009): 702–13. http://dx.doi.org/10.1128/jb.00680-09.

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ABSTRACT Conjugative transfer from Clostridium symbiosum to enterococci of Tn1549, which confers VanB-type vancomycin resistance, has been reported. This indicates the presence of a transfer origin (oriT) in the element. Transcription analysis of Tn1549 indicated that orf29, orf28, orfz, and orf27 were cotranscribed. A pACYC184 derivative containing 250 bp intergenic to orf29-orf30 of Tn1549 was mobilized in Escherichia coli recA::RP4::Δnic provided that orf28 and orf29 were delivered simultaneously. These open reading frame (ORF) genes were able to promote mobilization in trans, but a cis-acting preference was observed. On the basis of a mobilization assay, a minimal 28-bp oriT was delimited, although the frequency of transfer was significantly reduced compared to that of a 130-bp oriT fragment. The minimal oriT contained an inverted repeat and a core, which was homologous to the cleavage sequence found in certain Gram-positive rolling-circle replicating (RCR) plasmids. While Orf29 was a mobilization accessory component similar to MobC proteins, Orf28 was identified as a relaxase belonging to a new phyletic cluster of the MOBp superfamily. The nick site was identified within oriT by an oligonucleotide cleavage assay. Closely related oriTs linked to mobilization genes were detected in data banks; they were found in various integrative and conjugative elements (ICEs) originating mainly from anaerobes. These results support the notion that Tn1549 is a member of a MOBp clade. Interestingly, the Tn1549-derived constructs were mobilized by RP4 in E. coli, suggesting that a relaxosome resulting from DNA cleavage by Orf28 interacted with the coupling protein TraG. This demonstrates the capacity of Tn1549 to be mobilized by a heterologous transfer system.

6

Xia, Shuangluo, e Jon D. Robertus. "Effect of divalent ions on the minimal relaxase domain of MobA". Archives of Biochemistry and Biophysics 488, n. 1 (agosto 2009): 42–47. http://dx.doi.org/10.1016/j.abb.2009.06.004.

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van Kranenburg, Richard, e Willem M. de Vos. "Characterization of Multiple Regions Involved in Replication and Mobilization of Plasmid pNZ4000 Coding for Exopolysaccharide Production in Lactococcus lactis". Journal of Bacteriology 180, n. 20 (15 ottobre 1998): 5285–90. http://dx.doi.org/10.1128/jb.180.20.5285-5290.1998.

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ABSTRACT We characterized the regions involved in replication and mobilization of the 40-kb plasmid pNZ4000, encoding exopolysaccharide (EPS) production in Lactococcus lactis NIZO B40. The plasmid contains four highly conserved replication regions with homologous rep genes (repB1, repB2,repB3, and repB4) that belong to the lactococcal theta replicon family. Subcloning of each replicon individually showed that all are functional and compatible in L. lactis. Plasmid pNZ4000 and genetically labeled derivatives could be transferred to different L. lactis strains by conjugation, and pNZ4000 was shown to be a mobilization plasmid. Two regions involved in mobilization were identified near two of the replicons; both included an oriT sequence rich in inverted repeats. Conjugative mobilization of the nonmobilizable plasmid pNZ124 was promoted by either one of these oriT sequences, demonstrating their functionality. One oriT sequence was followed by a mobA gene, coding for atrans-acting protein, which increased the frequency of conjugative transfer 100-fold. The predicted MobA protein and theoriT sequences show protein and nucleotide similarity, respectively, with the relaxase and with the inverted repeat andnic site of the oriT from the Escherichia coli plasmid R64. The presence on pNZ4000 of four functional replicons, two oriT sequences, and several insertion sequence-like elements strongly suggests that this EPS plasmid is a naturally occurring cointegrate.

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Godziszewska, Jolanta, Gabriel Moncalián, Matilde Cabezas, Aneta A. Bartosik, Fernando de la Cruz e Grazyna Jagura-Burdzy. "Concerted action of NIC relaxase and auxiliary protein MobC in RA3 plasmid conjugation". Molecular Microbiology 101, n. 3 (2 giugno 2016): 439–56. http://dx.doi.org/10.1111/mmi.13401.

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Fernandez-Lopez, C., R. Pluta, R. Perez-Luque, L. Rodriguez-Gonzalez, M. Espinosa, M. Coll, F. Lorenzo-Diaz e D. R. Boer. "Functional Properties and Structural Requirements of the Plasmid pMV158-Encoded MobM Relaxase Domain". Journal of Bacteriology 195, n. 13 (26 aprile 2013): 3000–3008. http://dx.doi.org/10.1128/jb.02264-12.

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Monzingo, Arthur F., Angela Ozburn, Shuangluo Xia, Richard J. Meyer e Jon D. Robertus. "The Structure of the Minimal Relaxase Domain of MobA at 2.1 Å Resolution". Journal of Molecular Biology 366, n. 1 (febbraio 2007): 165–78. http://dx.doi.org/10.1016/j.jmb.2006.11.031.

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Lorenzo-Diaz, F., V. Solano-Collado, R. Lurz, A. Bravo e M. Espinosa. "Autoregulation of the Synthesis of the MobM Relaxase Encoded by the Promiscuous Plasmid pMV158". Journal of Bacteriology 194, n. 7 (27 gennaio 2012): 1789–99. http://dx.doi.org/10.1128/jb.06827-11.

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Fernández-López, Cris, Fabián Lorenzo-Díaz, Rosa Pérez-Luque, Lorena Rodríguez-González, Roeland Boer, Rudi Lurz, Alicia Bravo, Miquel Coll e Manuel Espinosa. "Nicking activity of the pMV158 MobM relaxase on cognate and heterologous origins of transfer". Plasmid 70, n. 1 (luglio 2013): 120–30. http://dx.doi.org/10.1016/j.plasmid.2013.03.004.

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Parker, Christopher, e Richard J. Meyer. "The R1162 relaxase/primase contains two, type IV transport signals that require the small plasmid protein MobB". Molecular Microbiology 66, n. 1 (ottobre 2007): 252–61. http://dx.doi.org/10.1111/j.1365-2958.2007.05925.x.

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Lorenzo-Díaz, Fabián, Lubomir Dostál, Miquel Coll, Joel F. Schildbach, Margarita Menéndez e Manuel Espinosa. "The MobM relaxase domain of plasmid pMV158: thermal stability and activity upon Mn2+ and specific DNA binding". Nucleic Acids Research 39, n. 10 (3 febbraio 2011): 4315–29. http://dx.doi.org/10.1093/nar/gkr049.

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Peed, Lindsay, Anita C. Parker e C. Jeffrey Smith. "Genetic and Functional Analyses of the mob Operon on Conjugative Transposon CTn341 from Bacteroides spp." Journal of Bacteriology 192, n. 18 (16 luglio 2010): 4643–50. http://dx.doi.org/10.1128/jb.00317-10.

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ABSTRACT Bacteroides are Gram-negative anaerobes indigenous to the intestinal tract of humans, and they are important opportunistic pathogens. Mobile genetic elements, such as conjugative transposons (CTns), have contributed to an increase in antibiotic resistance in these organisms. CTns are self-transmissible elements that belong to the superfamily of integrative and conjugative elements (ICEs). CTn341 is 52 kb; it encodes tetracycline resistance and its transfer is induced by tetracycline. The mobilization region of CTn341 was shown to be comprised of a three-gene operon, mobABC, and the transfer origin, oriT. The three genes code for a nicking accessory protein, a relaxase, and a VirD4-like coupling protein, respectively. The Mob proteins were predicted to mediate the formation of the relaxosome complex, nick DNA at the oriT, and shuttle the DNA/protein complex to the mating-pore apparatus. The results of mutational studies indicated that the three genes are required for maximal transfer of CTn341. Mob gene transcription was induced by tetracycline, and this regulation was mediated through the two-component regulatory system, RteAB. The oriT region of CTn341 was located within 100 bp of mobA, and a putative Bacteroides consensus nicking site was observed within this region. Mutation of the putative nick site resulted in a loss of transfer. This study demonstrated a role of the mobilization region for transfer of Bacteroides CTns and that tetracycline induction occurs for the mob gene operon, as for the tra gene operon(s), as shown previously.

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Ibrahim Al-Trad, Esra’a, Ainal Mardziah Che Hamzah, Chew Chieng Yeo, Suat Moi Puah, Kek Heng Chua e Ching Hoong Chew. "Whole Genome Sequencing of a Clinical Methicillin-Resistant Staphylococcus aureus from Terengganu Led to the Discovery of a Novel 58.4 kb Conjugative Plasmid". Asian Journal of Medicine and Biomedicine 6, S1 (9 novembre 2022): 87–88. http://dx.doi.org/10.37231/ajmb.2022.6.s1.539.

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Methicillin-resistant Staphylococcus aureus (MRSA) has been listed by the World Health Organization as a priority antibiotic-resistant nosocomial pathogen in urgent need of new antimicrobials [1]. Plasmids are a key factor in the pathology and epidemiology of MRSA isolates and play important roles in their evolution. In our on-going efforts to better understand the genetic background and molecular epidemiology of MRSA isolates from Terengganu, Malaysia, whole genome sequencing using Illumina HiSeq platform (HiSeq-PE150) was performed on a 31 selection of clinical isolates obtained from the main tertiary hospital, Hospital Sultanah Nur Zahirah (HSNZ). One of these isolates, designated S. aureus SauR23, was isolated from pus in 2016 and was resistant to seven classes of antimicrobials and thus categorized as multidrug resistant (MDR). Analysis of the genome sequence of SauR23 showed it belonged to the ST22 clone with a SCCmec class IV(2B) and harbored the blaZ, mecA, norA, lmrS, mepR and ermC resistance genes, which corresponded to its MDR phenotype. Besides the norA-encoded efflux pump, fluoroquinolone resistance in SauR23 could also be due to the S84L point mutation in its gyrA-encoded DNA gyrase. SauR23 was found to carry three plasmids, designated pSauR23-1 (58,422 bp), pSauR23-2 (3,011 bp), and pSauR23-3 (2,473 bp). The smallest plasmid, pSauR23-3 was a RepL-family plasmid that encoded the ermC gene and was likely responsible for the inducible macrolide-lincosamide-streptogrammin B (iMLSB) phenotype exhibited by the host strain. Plasmid pSauR23-2 was a Rep_1 family small cryptic plasmid. On the other hand, pSauR23-1 is a novel, potentially conjugative plasmid that contains a replicase of the RepA_N domain (repUS20) that shared low sequence identity (34%) to the RepA_N replicase of pWBG749, a known staphylococcal conjugative plasmid. The putative conjugative region of pSauR23-1 differed from the conjugative transfer system of pWBG749 as well as other known conjugative systems in the database. Nevertheless, genes which contained conserved motifs for the MobL relaxase, the TraG/TraD-like conjugative transfer protein, and a type VI secretion system ATPase were detected within this region of the plasmid.

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Whitaker, Neal, Yuqing Chen, Simon J. Jakubowski, Mayukh K. Sarkar, Feng Li e Peter J. Christie. "The All-Alpha Domains of Coupling Proteins from the Agrobacterium tumefaciens VirB/VirD4 and Enterococcus faecalis pCF10-Encoded Type IV Secretion Systems Confer Specificity to Binding of Cognate DNA Substrates". Journal of Bacteriology 197, n. 14 (4 maggio 2015): 2335–49. http://dx.doi.org/10.1128/jb.00189-15.

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ABSTRACTBacterial type IV coupling proteins (T4CPs) bind and mediate the delivery of DNA substrates through associated type IV secretion systems (T4SSs). T4CPs consist of a transmembrane domain, a conserved nucleotide-binding domain (NBD), and a sequence-variable helical bundle called the all-alpha domain (AAD). In the T4CP structural prototype, plasmid R388-encoded TrwB, the NBD assembles as a homohexamer resembling RecA and DNA ring helicases, and the AAD, which sits at the channel entrance of the homohexamer, is structurally similar to N-terminal domain 1 of recombinase XerD. Here, we defined the contributions of AADs from theAgrobacterium tumefaciensVirD4 andEnterococcus faecalisPcfC T4CPs to DNA substrate binding. AAD deletions abolished DNA transfer, whereas production of the AAD in otherwise wild-type donor strains diminished the transfer of cognate but not heterologous substrates. Reciprocal swaps of AADs between PcfC and VirD4 abolished the transfer of cognate DNA substrates, although strikingly, the VirD4-AADPcfCchimera (VirD4 with the PcfC AAD) supported the transfer of a mobilizable plasmid. Purified AADs from both T4CPs bound DNA substrates without sequence preference but specifically bound cognate processing proteins required for cleavage at origin-of-transfer sequences. The soluble domains of VirD4 and PcfC lacking their AADs neither exerted negative dominancein vivonor specifically bound cognate processing proteinsin vitro. Our findings support a model in which the T4CP AADs contribute to DNA substrate selection through binding of associated processing proteins. Furthermore, MOBQ plasmids have evolved a docking mechanism that bypasses the AAD substrate discrimination checkpoint, which might account for their capacity to promiscuously transfer through many different T4SSs.IMPORTANCEFor conjugative transfer of mobile DNA elements, members of the VirD4/TraG/TrwB receptor superfamily bind cognate DNA substrates through mechanisms that are largely undefined. Here, we supply genetic and biochemical evidence that a helical bundle, designated the all-alpha domain (AAD), of T4SS receptors functions as a substrate specificity determinant. We show that AADs from two substrate receptors,Agrobacterium tumefaciensVirD4 andEnterococcus faecalisPcfC, bind DNA without sequence or strand preference but specifically bind the cognate relaxases responsible for nicking and piloting the transferred strand through the T4SS. We propose that interactions of receptor AADs with DNA-processing factors constitute a basis for selective coupling of mobile DNA elements with type IV secretion channels.

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Ni, Kai, Bo Che, Rong Gu, Chunhong Wang, Hongyang Xu, Huiduo Li, Shiyan Cen, Mingzhi Luo e Linhong Deng. "BitterDB database analysis plus cell stiffness screening identify flufenamic acid as the most potent TAS2R14-based relaxant of airway smooth muscle cells for therapeutic bronchodilation". Theranostics 14, n. 4 (2024): 1744–63. http://dx.doi.org/10.7150/thno.92492.

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Laroussi, Haifa, Yanis Aoudache, Emilie Robert, Virginie Libante, Louise Thiriet, Dominique Mias-Lucquin, Badreddine Douzi et al. "Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria". Nucleic Acids Research, 18 luglio 2022. http://dx.doi.org/10.1093/nar/gkac607.

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Abstract Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that recognize the binding site of oriT sequence and nick at a conserved nic site. The ICESt3/Tn916/ICEBs1 superfamily, which is widespread among Firmicutes, encodes uncanonical relaxases belonging to a recently identified family called MOBT. This family is related to the rolling circle replication initiators of the Rep_trans family. The nic site of these MOBT relaxases is conserved but their DNA binding site is still unknown. Here, we identified the bind site of RelSt3, the MOBT relaxase from ICESt3. Unexpectedly, we found this bind site distantly located from the nic site. We revealed that the binding of the RelSt3 N-terminal HTH domain is required for efficient nicking activity. We also deciphered the role of RelSt3 in the initial and final stages of DNA processing during conjugation. Especially, we demonstrated a strand transfer activity, and the formation of covalent DNA-relaxase intermediate for a MOBT relaxase.

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Soler, Nicolas, Emilie Robert, Isaure Chauvot de Beauchêne, Philippe Monteiro, Virginie Libante, Bernard Maigret, Johan Staub et al. "Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs". Mobile DNA 10, n. 1 (3 maggio 2019). http://dx.doi.org/10.1186/s13100-019-0160-9.

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Añorga, Maite, Miriam Urriza, Cayo Ramos e Jesús Murillo. "Multiple relaxases contribute to the horizontal transfer of the virulence plasmids from the tumorigenic bacterium Pseudomonas syringae pv. savastanoi NCPPB 3335". Frontiers in Microbiology 13 (12 dicembre 2022). http://dx.doi.org/10.3389/fmicb.2022.1076710.

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Pseudomonas syringae pv. savastanoi NCPPB 3335 is the causal agent of olive knot disease and contains three virulence plasmids: pPsv48A (pA), 80 kb; pPsv48B (pB), 45 kb, and pPsv48C (pC), 42 kb. Here we show that pB contains a complete MPFT (previously type IVA secretion system) and a functional origin of conjugational transfer adjacent to a relaxase of the MOBP family; pC also contains a functional oriT-MOBP array, whereas pA contains an incomplete MPFI (previously type IVB secretion system), but not a recognizable oriT. Plasmid transfer occurred on solid and in liquid media, and on leaf surfaces of a non-host plant (Phaseolus vulgaris) with high (pB) or moderate frequency (pC); pA was transferred only occasionally after cointegration with pB. We found three plasmid-borne and three chromosomal relaxase genes, although the chromosomal relaxases did not contribute to plasmid dissemination. The MOBP relaxase genes of pB and pC were functionally interchangeable, although with differing efficiencies. We also identified a functional MOBQ mobilization region in pC, which could only mobilize this plasmid. Plasmid pB could be efficiently transferred to strains of six phylogroups of P. syringae sensu lato, whereas pC could only be mobilized to two strains of phylogroup 3 (genomospecies 2). In two of the recipient strains, pB was stably maintained after 21 subcultures in liquid medium. The carriage of several relaxases by the native plasmids of P. syringae impacts their transfer frequency and, by providing functional diversity and redundancy, adds robustness to the conjugation system.

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Zeng, Zhu, Lei Lei, Linman Li, Shengni Hua, Wenting Li, Limei Zhang, Qiuping Lin et al. "In silico characterization of blaNDM-harboring plasmids in Klebsiella pneumoniae". Frontiers in Microbiology 13 (23 novembre 2022). http://dx.doi.org/10.3389/fmicb.2022.1008905.

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Klebsiella pneumoniae is a primary culprit of antibiotic-resistant nosocomial infections worldwide, and infections caused by NDM-producing strains are a major threat due to limited therapeutic options. The majority of blaNDM cases occur on plasmids; therefore, we explored the relationships between plasmids and blaNDM genes in K. pneumoniae by analyzing the variants of blaNDM, replicon types, conjugative transfer regions of 171 blaNDM-harboring plasmids from 4,451 K. pneumoniae plasmids. Of the nine identified blaNDM variants, blaNDM-1 (73.68%) and blaNDM-5 (16.37%) were the most dominant. Over half of the blaNDM-harboring plasmids of K. pneumoniae were classified into IncF plasmids. IncX3 single-replicon plasmids (46–57 kb) carried genes encoding relaxases of the MOBP family, T4CP genes of the VirD4/TraG subfamily, and VirB-like T4SS gene clusters, which were mainly geographically distributed in China. We found 10 blaNDM-harboring IncN plasmids (38.38–63.05 kb) carrying the NW-type origin of transfer (oriT) regions, genes coding for relaxases of MOBF family, genes encoding T4CPs of the TrwB/TraD subfamily, and Trw-like T4SS gene clusters, which were also mainly geographically distributed in China. Moreover, we identified 21 IncC plasmids carrying blaNDM-1 (140.1–329.2 kb), containing the A/C-type oriTs, genes encoding relaxases of MOBH family, genes encoding T4CPs belonging to TrwB/TraD subfamily, and Tra_F-like T4SS gene clusters. The blaNDM-harboring IncC plasmids were widely geographically distributed all over the world, mainly in the United States, China and Viet Nam. These findings enhance our understanding of the diversity of blaNDM-harboring plasmids in K. pneumoniae.

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Lorenzo-Díaz, Fabián, Cris Fernández-López, Beatriz Guillén-Guío, Alicia Bravo e Manuel Espinosa. "Relaxase MobM Induces a Molecular Switch at Its Cognate Origin of Transfer". Frontiers in Molecular Biosciences 5 (26 febbraio 2018). http://dx.doi.org/10.3389/fmolb.2018.00017.

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Gustavson, Kristin, George Davey Smith e Espen M. Eilertsen. "Handling unobserved confounding in the relation between prenatal risk factors and child outcomes: a latent variable strategy". European Journal of Epidemiology, 26 marzo 2022. http://dx.doi.org/10.1007/s10654-022-00857-6.

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Abstract Background Several studies have examined maternal health behavior during pregnancy and child outcomes. Negative control variables have been used to address unobserved confounding in such studies. This approach assumes that confounders affect the exposure and the negative control to the same degree. The current study introduces a novel latent variable approach that relaxes this assumption by accommodating repeated measures of maternal health behavior during pregnancy. Methods Monte Carlo simulations were used to examine the performance of the latent variable approach. A real-life example is also provided, using data from the Norwegian Mother, Father, and Child Study (MoBa). Results Simulations: Regular regression analyses without a negative control variable worked poorly in the presence of unobserved confounding. Including a negative control variable improved result substantially. The latent variable approach provided unbiased results in several situations where the other analysis models worked poorly. Real-life data: Maternal alcohol use in the first trimester was associated with increased ADHD symptoms in the child in the standard regression model. This association was not present in the latent variable approach. Conclusion The current study showed that a latent variable approach with a negative control provided unbiased estimates of causal associations between repeated measures of maternal health behavior during pregnancy and child outcomes, even when the effect of the confounder differed in magnitude between the negative control and the exposures. The real-life example showed that inferences from the latent variable approach were incompatible with those from the standard regression approach. Limitations of the approach are discussed.

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Yu, Zhijian, Zhengrong Zhang, Lile Shi, Shengni Hua, Ting Luan, Qiuping Lin, Zhixiong Zheng, Xiaosan Feng, Mubiao Liu e Xiaobin Li. "In silico characterization of IncX3 plasmids carrying blaOXA-181 in Enterobacterales". Frontiers in Cellular and Infection Microbiology 12 (8 settembre 2022). http://dx.doi.org/10.3389/fcimb.2022.988236.

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Carbapenem-resistant Enterobacterales poses a global urgent antibiotic resistance threat because of its ability to transfer carbapenemase genes to other bacteria via horizontal gene transfer mediated by mobile genetic elements such as plasmids. Oxacillinase-181 (OXA-181) is one of the most common OXA-48-like carbapenemases, and OXA-181-producing Enterobacterales has been reported in many countries worldwide. However, systematic research concerning the overall picture of plasmids harboring blaOXA-181 in Enterobacterales is currently scarce. In this study, we aimed to determine the phylogeny and evolution of blaOXA-181-positive (gene encoding OXA-181) plasmids. To characterize the plasmids harboring blaOXA-181 in Enterobacterales, we identified 81 blaOXA-181-positive plasmids from 35,150 bacterial plasmids downloaded from the NCBI RefSeq database. Our results indicated that diverse plasmid types harbored blaOXA-181 but was predominantly carried by IncX3-type plasmids. We systematically compared the host strains, plasmid types, conjugative transfer regions, and genetic contexts of blaOXA-181 among the 66 blaOXA-181-positive IncX3 plasmids. We found that IncX3 plasmids harboring blaOXA-181 were mostly ColKP3-IncX3 hybrid plasmids with a length of 51 kb each and were mainly distributed in Escherichia coli and Klebsiella pneumoniae. Most of the IncX3 plasmids harboring blaOXA-181 were human origin. Almost all the blaOXA-181-positive IncX3 plasmids were found to carry genes coding for relaxases of the MOBP family and VirB-like type IV secretion system (T4SS) gene clusters, and all the 66 IncX3 plasmids were found to carry the genes encoding type IV coupling proteins (T4CPs) of the VirD4/TraG subfamily. Most IncX3 plasmids harbored both blaOXA-181 and qnrS1 in their genomes, and the two antibiotic resistance genes were found to a composite transposon bracketed by two copies of insertion sequence IS26 in the same orientation. Our findings provide important insights into the phylogeny and evolution of blaOXA-181-positive IncX3 plasmids and further address their role in acquiring and spreading blaOXA-181 genes in Enterobacterales.

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