Crystal Structures of the F and pSLT Plasmid TraJ N-Terminal Regions Reveal Similar Homodimeric PAS Folds with Functional Interchangeability

Lu, Jun; Wu, R.; Adkins, Joshua N.; Joachimiak, A.; Glover, J. N. Mark

doi:10.1021/bi500244m

Cited by 7 publications

(15 citation statements)

References 56 publications

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“…However, in TraJ V the HTH domain is located in the N-terminal half of the protein. A comparison between the predicted 3D structure for TraJ V N-terminal domain and the solved structure for F plasmid TraJ N-terminal domain (pdb 4KQD) (Lu et al, 2014) showed no structural homology (Figure 5C). In fact, TraJ is predicted to be similar to the canonical LuxR protein, with an N-terminal effector binding domain and a C-terminal DBD.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics of the Conjugation Region of F-like Plasmids: Five Shades of F

Fernández-López

Toro

Moncalián

et al. 2016

Front. Mol. Biosci.

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The F plasmid is the foremost representative of a large group of conjugative plasmids, prevalent in Escherichia coli, and widely distributed among the Enterobacteriaceae. These plasmids are of clinical relevance, given their frequent association with virulence determinants, colicins, and antibiotic resistance genes. Originally defined by their sensitivity to certain male-specific phages, IncF plasmids share a conserved conjugative system and regulatory circuits. In order to determine whether the genetic architecture and regulation circuits are preserved among these plasmids, we analyzed the natural diversity of F-like plasmids. Using the relaxase as a phylogenetic marker, we identified 256 plasmids belonging to the IncF/ MOBF12group, present as complete DNA sequences in the NCBI database. By comparative genomics, we identified five major groups of F-like plasmids. Each shows a particular operon structure and alternate regulatory systems. Results show that the IncF/MOBF12 conjugation gene cluster conforms a diverse and ancient group, which evolved alternative regulatory schemes in its adaptation to different environments and bacterial hosts.

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Section: Resultsmentioning

confidence: 99%

Comparative Genomics of the Conjugation Region of F-like Plasmids: Five Shades of F

Fernández-López

Toro

Moncalián

et al. 2016

Front. Mol. Biosci.

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“…The putative TraJ-binding inverted repeats in the F, R1, and R100 plasmids share little sequence homology, consistent with the previous finding that TraJ exclusively acts on its cognate P Y among these three plasmids. In contrast, the putative TraJ-binding repeats in R1 and pSLT plasmids are quite similar, explaining the cross-activity of TraJ between these two F-like plasmids (11,16).…”

Section: Figmentioning

confidence: 97%

“…Activation of P Y requires TraJ, a transcriptional activator encoded by the gene immediately upstream of the tra operon (14), and the activity of P Y is a function of the TraJ level (8). TraJ has an N-terminal PAS (Per-Arnt-Sim) domain responsible for dimerization and a C-terminal helix-turn-helix (HTH) motif that carries allelic specificity in recognizing its cognate plasmid DNA (11,(15)(16)(17). A previous DNase I footprinting experiment indicated that TraJ specifically binds to an inverted repeat sequence immediately upstream of the Ϫ35 region of P Y in the F-like plasmid R100 (18).…”

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confidence: 99%

Cooperative Function of TraJ and ArcA in Regulating the F Plasmid tra Operon

Peng

Wan

et al. 2019

J Bacteriol

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The F plasmid tra operon encodes most of the proteins required for bacterial conjugation. TraJ and ArcA are known activators of the tra operon promoter PY, which is subject to H-NS-mediated silencing. Donor ability and promoter activity assays indicated that PY is inactivated by silencers and requires both TraJ and ArcA for activation to support efficient F conjugation. The observed low-level, ArcA-independent F conjugation is caused by tra expression from upstream alternative promoters. Electrophoretic mobility shift assays showed that TraJ alone weakly binds to PY regulatory DNA; however, TraJ binding is significantly enhanced by ArcA binding to the same DNA, indicating cooperativity of the two proteins. Analysis of binding affinities between ArcA and various DNA fragments in the PY regulatory region defined a 22-bp tandem repeat sequence (from −76 to −55 of PY) sufficient for optimal ArcA binding, which is immediately upstream of the predicted TraJ-binding site (from −54 to −34). Deletion analysis of the PY promoter in strains deficient in TraJ, ArcA, and/or H-NS determined that sequences upstream of −103 are required by silencers including H-NS for PY silencing, whereas sequences downstream of −77 are targeted by TraJ and ArcA for activation. TraJ and ArcA appear not only to counteract PY silencers but also to directly activate PY in a cooperative manner. Our data reveal the cooperativity of TraJ and ArcA during PY activation and provide insights into the regulatory circuit controlling F-family plasmid-mediated bacterial conjugation. IMPORTANCE Conjugation is a major mechanism for dissemination of antibiotic resistance and virulence among bacterial populations. The tra operon in the F family of conjugative plasmids encodes most of the proteins involved in bacterial conjugation. This work reveals that activation of tra operon transcription requires two proteins, TraJ and ArcA, to bind cooperatively to adjacent sites immediately upstream of the major tra promoter PY. The interaction of TraJ and ArcA with the tra operon not only relieves PY from silencers but also directly activates it. These findings provide insights into the regulatory circuit of the F-family plasmid-mediated bacterial conjugation.

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“…TraJ contains a second domain that represents the DNA-binding part of the protein as suggested by the presence of a helix-turn-helix DNA-binding motif. It was also shown that this domain, located in the C-terminal half of TraJ, confers DNA-binding specificity (134). Both the PAS domain and the DNA-binding domain are essential for the function of TraJ (135), which also served to define subgroups within the group of MOB F12 A plasmids (see Table 1).…”

Section: Regulation Of Dna Transfer Genes: On and Off Switchesmentioning

confidence: 99%

“…Both the PAS domain and the DNA-binding domain are essential for the function of TraJ (135), which also served to define subgroups within the group of MOB F12 A plasmids (see Table 1). Importantly, the sequence differences between TraJ proteins result in plasmid subgroup-specific activation of the P Y promoter which differs in the proposed sequence (centered at −44 relative to the transcription start site) that is likely contacted by TraJ (15,128,134). Therefore, in situations where two compatible F-like plasmids reside in the same cell, TraJ escape from FinOP in one plasmid would result in transfer gene activation and subsequent DNA transfer of only one of the two plasmids.…”

Section: Regulation Of Dna Transfer Genes: On and Off Switchesmentioning

confidence: 99%

Spread and Persistence of Virulence and Antibiotic Resistance Genes: A Ride on the F Plasmid Conjugation Module

Koraimann

2018

EcoSal Plus

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The F plasmid or F-factor is a large, 100-kbp, circular conjugative plasmid of and was originally described as a vector for horizontal gene transfer and gene recombination in the late 1940s. Since then, F and related F-like plasmids have served as role models for bacterial conjugation. At present, more than 200 different F-like plasmids with highly related DNA transfer genes, including those for the assembly of a type IV secretion apparatus, are completely sequenced. They belong to the phylogenetically related MOBA group. F-like plasmids are present in enterobacterial hosts isolated from clinical as well as environmental samples all over the world. As conjugative plasmids, F-like plasmids carry genetic modules enabling plasmid replication, stable maintenance, and DNA transfer. In this plasmid backbone of approximately 60 kbp, the DNA transfer genes occupy the largest and mostly conserved part. Subgroups of MOBA plasmids can be defined based on the similarity of TraJ, a protein required for DNA transfer gene expression. In addition, F-like plasmids harbor accessory cargo genes, frequently embedded within transposons and/or integrons, which harness their host bacteria with antibiotic resistance and virulence genes, causing increasingly severe problems for the treatment of infectious diseases. Here, I focus on key genetic elements and their encoded proteins present on the F-factor and other typical F-like plasmids belonging to the MOBA group of conjugative plasmids.

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Crystal Structures of the F and pSLT Plasmid TraJ N-Terminal Regions Reveal Similar Homodimeric PAS Folds with Functional Interchangeability

Cited by 7 publications

References 56 publications

Comparative Genomics of the Conjugation Region of F-like Plasmids: Five Shades of F

Comparative Genomics of the Conjugation Region of F-like Plasmids: Five Shades of F

Cooperative Function of TraJ and ArcA in Regulating the F Plasmid tra Operon

Spread and Persistence of Virulence and Antibiotic Resistance Genes: A Ride on the F Plasmid Conjugation Module

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