Conjugation in Gram-Positive Bacteria
- Authors: Nikolaus Goessweiner-Mohr1, Karsten Arends2, Walter Keller3, Elisabeth Grohmann4
- Editors: Marcelo E. Tolmasky6, Juan Carlos Alonso7
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VIEW AFFILIATIONS HIDE AFFILIATIONSAffiliations: 1: Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; 2: Robert Koch-Institute, Nordufer 20, 13353 Berlin, Germany; 3: Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; 4: Faculty of Biology, Microbiology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; 5: Division of Infectious Diseases, University Medical Centre Freiburg, 79106 Freiburg, Germany; 6: California State University, Fullerton, CA; 7: Centro Nacional de Biotecnología, Cantoblanco, Madrid, Spain
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Received 14 November 2013 Accepted 16 December 2013 Published 15 August 2014
- Correspondence: Elisabeth Grohmann, elisabeth.grohmann@uniklinik-freiburg.de

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Abstract:
Conjugative transfer is the most important means of spreading antibiotic resistance and virulence factors among bacteria. The key vehicles of this horizontal gene transfer are a group of mobile genetic elements, termed conjugative plasmids. Conjugative plasmids contain as minimum instrumentation an origin of transfer (oriT), DNA-processing factors (a relaxase and accessory proteins), as well as proteins that constitute the trans-envelope transport channel, the so-called mating pair formation (Mpf) proteins. All these protein factors are encoded by one or more transfer (tra) operons that together form the DNA transport machinery, the Gram-positive type IV secretion system. However, multicellular Gram-positive bacteria belonging to the streptomycetes appear to have evolved another mechanism for conjugative plasmid spread reminiscent of the machinery involved in bacterial cell division and sporulation, which transports double-stranded DNA from donor to recipient cells. Here, we focus on the protein key players involved in the plasmid spread through the two different modes and present a new secondary structure homology-based classification system for type IV secretion protein families. Moreover, we discuss the relevance of conjugative plasmid transfer in the environment and summarize novel techniques to visualize and quantify conjugative transfer in situ.
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Citation: Goessweiner-Mohr N, Arends K, Keller W, Grohmann E. 2014. Conjugation in Gram-Positive Bacteria. Microbiol Spectrum 2(4):PLAS-0004-2013. doi:10.1128/microbiolspec.PLAS-0004-2013.




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Abstract:
Conjugative transfer is the most important means of spreading antibiotic resistance and virulence factors among bacteria. The key vehicles of this horizontal gene transfer are a group of mobile genetic elements, termed conjugative plasmids. Conjugative plasmids contain as minimum instrumentation an origin of transfer (oriT), DNA-processing factors (a relaxase and accessory proteins), as well as proteins that constitute the trans-envelope transport channel, the so-called mating pair formation (Mpf) proteins. All these protein factors are encoded by one or more transfer (tra) operons that together form the DNA transport machinery, the Gram-positive type IV secretion system. However, multicellular Gram-positive bacteria belonging to the streptomycetes appear to have evolved another mechanism for conjugative plasmid spread reminiscent of the machinery involved in bacterial cell division and sporulation, which transports double-stranded DNA from donor to recipient cells. Here, we focus on the protein key players involved in the plasmid spread through the two different modes and present a new secondary structure homology-based classification system for type IV secretion protein families. Moreover, we discuss the relevance of conjugative plasmid transfer in the environment and summarize novel techniques to visualize and quantify conjugative transfer in situ.

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Figures
Genetic organization of the pIP501 tra operon. Proteins with sequence similarities with the corresponding A. tumefaciens Ti-plasmid VirB/D4, E. faecalis pCF10, and C. perfringens pCW3 T4SS proteins are in blue; the potential two-protein-coupling protein (consisting of TraIpIP501 and TraJpIP501) is indicated with brackets; relations based on structure (TraM C-terminal domain, VirB8-like [ 54 ]) and domain prediction (TraL, VirB6-like) based similarities are in yellow; the gene encoding the putative relaxase is in green. The respective protein families are indicated. Ptra, tra operon promoter. The genes of the pIP501 tra region are drawn to scale. Put., putative. doi:10.1128/microbiolspec.PLAS-0004-2013.f1.

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FIGURE 1
Genetic organization of the pIP501 tra operon. Proteins with sequence similarities with the corresponding A. tumefaciens Ti-plasmid VirB/D4, E. faecalis pCF10, and C. perfringens pCW3 T4SS proteins are in blue; the potential two-protein-coupling protein (consisting of TraIpIP501 and TraJpIP501) is indicated with brackets; relations based on structure (TraM C-terminal domain, VirB8-like [ 54 ]) and domain prediction (TraL, VirB6-like) based similarities are in yellow; the gene encoding the putative relaxase is in green. The respective protein families are indicated. Ptra, tra operon promoter. The genes of the pIP501 tra region are drawn to scale. Put., putative. doi:10.1128/microbiolspec.PLAS-0004-2013.f1.
Model of the pIP501 DNA transfer pathway. First, oriT pIP501 is bound by the relaxase TraA. After being nicked, the single-stranded plasmid is recruited to the putative transfer channel (modified from reference 17) via the putative two-protein coupling protein TraJ. Decreased shading of PG symbolizes TraG-mediated local opening of PG. The localization and orientation of the T4SS proteins is based on in silico predictions and localization studies ( 52 , 54 ). The N terminus of the T4SS proteins is marked (N). Arrows indicate protein-protein interactions determined by yeast-two-hybrid studies and validated by pull-down assays ( 27 ), as well as interactions found by using the Thermofluor method (Goessweiner-Mohr et al., unpublished data). The thickness of the arrows marks the strength of the detected interactions. The putative function of key members of the pIP501 tra operon in the DNA secretion process is indicated. PG, peptidoglycan; CM, cytoplasmic membrane; CP, cytoplasm. doi:10.1128/microbiolspec.PLAS-0004-2013.f2.

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FIGURE 2
Model of the pIP501 DNA transfer pathway. First, oriT pIP501 is bound by the relaxase TraA. After being nicked, the single-stranded plasmid is recruited to the putative transfer channel (modified from reference 17) via the putative two-protein coupling protein TraJ. Decreased shading of PG symbolizes TraG-mediated local opening of PG. The localization and orientation of the T4SS proteins is based on in silico predictions and localization studies ( 52 , 54 ). The N terminus of the T4SS proteins is marked (N). Arrows indicate protein-protein interactions determined by yeast-two-hybrid studies and validated by pull-down assays ( 27 ), as well as interactions found by using the Thermofluor method (Goessweiner-Mohr et al., unpublished data). The thickness of the arrows marks the strength of the detected interactions. The putative function of key members of the pIP501 tra operon in the DNA secretion process is indicated. PG, peptidoglycan; CM, cytoplasmic membrane; CP, cytoplasm. doi:10.1128/microbiolspec.PLAS-0004-2013.f2.
Comparison of the domain arrangement and classification of putative lytic transglycosylases from G+ and G– putative T4SSs. TraG (pIP501), TcpG (pCW3), VirB1 (Ti-plasmid), and PrgK (pCF10) were chosen as representatives of their respective classes. The potential SLT and CHAP(-like) domains were assigned according to secondary structure predictions with PSIPred ( 131 ). TMHs were annotated with HMMTOP ( 53 ). doi:10.1128/microbiolspec.PLAS-0004-2013.f3.

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FIGURE 3
Comparison of the domain arrangement and classification of putative lytic transglycosylases from G+ and G– putative T4SSs. TraG (pIP501), TcpG (pCW3), VirB1 (Ti-plasmid), and PrgK (pCF10) were chosen as representatives of their respective classes. The potential SLT and CHAP(-like) domains were assigned according to secondary structure predictions with PSIPred ( 131 ). TMHs were annotated with HMMTOP ( 53 ). doi:10.1128/microbiolspec.PLAS-0004-2013.f3.
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.

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FIGURE 4a
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.

Click to view
FIGURE 4b
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.

Click to view
FIGURE 4c
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.

Click to view
FIGURE 4d
Secondary structure-based classification of lytic transglycosylases. A, class α, B, class β, C, class γ, D, class δ lytic transglycosylases. Secondary structure (PSIpred) and TM motif (HMMTOP) prediction for G– and G+ lytic transglycosylases from conjugative plasmids, transposons, ICEs, and GIs; alpha helices (blue), beta strands (red), and TM motifs (boxes) are highlighted; the putative N-terminal ends of the SLT and CHAP(-like) domains are indicated. doi:10.1128/microbiolspec.PLAS-0004-2013.f4.
Comparison of the domain arrangement and classification of VirB6-like proteins from G+ and G– putative T4SSs. TraL (pIP501), PrgH (pCF10), TcpH (pCW3), VirB6 (Ti-plasmid), TraD (pKM101), TraG (R1 plasmid), and TrbP (pBP136) were selected as representatives of their respective classes. Predicted TMHs (HMMTOP [ 53 ]) are represented as grey boxes. doi:10.1128/microbiolspec.PLAS-0004-2013.f5.

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FIGURE 5
Comparison of the domain arrangement and classification of VirB6-like proteins from G+ and G– putative T4SSs. TraL (pIP501), PrgH (pCF10), TcpH (pCW3), VirB6 (Ti-plasmid), TraD (pKM101), TraG (R1 plasmid), and TrbP (pBP136) were selected as representatives of their respective classes. Predicted TMHs (HMMTOP [ 53 ]) are represented as grey boxes. doi:10.1128/microbiolspec.PLAS-0004-2013.f5.
Tables
Classification of TraG-like and other lytic transglycosylases

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TABLE 1
Classification of TraG-like and other lytic transglycosylases
Supplemental Material
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