Yun CS, Suzuki C, Naito K, Takeda T, Takahashi Y, Sai F et al. Pmr, a histone-like protein H1 (H-NS) family protein encoded by the IncP-7 plasmid pCAR1, is a key global regulator that alters host function. J Bacteriol 192: 4720-4731

Biotechnology Research Center and Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Journal of bacteriology (Impact Factor: 2.81). 09/2010; 192(18):4720-31. DOI: 10.1128/JB.00591-10
Source: PubMed

ABSTRACT Histone-like protein H1 (H-NS) family proteins are nucleoid-associated proteins (NAPs) conserved among many bacterial species. The IncP-7 plasmid pCAR1 is transmissible among various Pseudomonas strains and carries a gene encoding the H-NS family protein, Pmr. Pseudomonas putida KT2440 is a host of pCAR1, which harbors five genes encoding the H-NS family proteins PP_1366 (TurA), PP_3765 (TurB), PP_0017 (TurC), PP_3693 (TurD), and PP_2947 (TurE). Quantitative reverse transcription-PCR (qRT-PCR) demonstrated that the presence of pCAR1 does not affect the transcription of these five genes and that only pmr, turA, and turB were primarily transcribed in KT2440(pCAR1). In vitro pull-down assays revealed that Pmr strongly interacted with itself and with TurA, TurB, and TurE. Transcriptome comparisons of the pmr disruptant, KT2440, and KT2440(pCAR1) strains indicated that pmr disruption had greater effects on the host transcriptome than did pCAR1 carriage. The transcriptional levels of some genes that increased with pCAR1 carriage, such as the mexEF-oprN efflux pump genes and parI, reverted with pmr disruption to levels in pCAR1-free KT2440. Transcriptional levels of putative horizontally acquired host genes were not altered by pCAR1 carriage but were altered by pmr disruption. Identification of genome-wide Pmr binding sites by ChAP-chip (chromatin affinity purification coupled with high-density tiling chip) analysis demonstrated that Pmr preferentially binds to horizontally acquired DNA regions. The Pmr binding sites overlapped well with the location of the genes differentially transcribed following pmr disruption on both the plasmid and the chromosome. Our findings indicate that Pmr is a key factor in optimizing gene transcription on pCAR1 and the host chromosome.

Download full-text


Available from: Masatoshi Miyakoshi, Sep 28, 2015
34 Reads
  • Source
    • "This strain cannot tolerate the loss of both MvaT and MvaU because it results in the induction of Pf4 phage, which superinfects and kills cells or inhibits their growth [23]. Conversely, P. putida KT2440 has five genes encoding MvaT-like proteins, turA-E, although transcriptional levels of turC, turD, and turE were considerably lower than those of turA and turB [24]–[27]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Enterobacterial H-NS-like proteins and Pseudomonas MvaT-like proteins share low homology at the amino acid sequence level, but both can function as xenogeneic silencers and are included in the H-NS family of proteins. H-NS family members have dimerization/oligomerization and DNA-binding domains connected by a flexible linker and form large nucleoprotein complexes using both domains. Pmr, an MvaT-like protein encoded on the IncP-7 carbazole-degradative plasmid pCAR1, is a key regulator of an interaction between pCAR1 and its host Pseudomonas putida KT2440. KT2440 has two transcribed genes that encode the MvaT-like proteins TurA and TurB. Our previous transcriptome analyses suggested that the functions of Pmr, TurA and TurB are non-equivalent, although the detailed underlying mechanisms remain unclear. In this study, we focused on the protein-protein interactions of Pmr, and assessed the homo-oligomerization capacity of various substituted and truncated Pmr derivatives by protein-protein cross-linking analysis. Six of the seven residues identified as important for homo-oligomerization in Pmr were located near the N-terminus, and the putative flexible linker or the region near that was not involved in homo-oligomerization, suggesting that Pmr homo-oligomerization is different from that of enterobacterial H-NS and that the functional mechanism differs between H-NS-like and MvaT-like proteins. In addition, we assessed homo- and hetero-oligomerization of Pmr by surface plasmon resonance analysis and found that the coupling ratio of TurB-Pmr oligomers is smaller than that of Pmr-Pmr or TurA-Pmr oligomers. These results raised the possibility that composition of the hetero-oligomers of Pmr, TurA, and TurB could explain why the different gene sets were affected by either pmr, turA, or turB disruption in our previous studies.
    PLoS ONE 08/2014; 9(8):e105656. DOI:10.1371/journal.pone.0105656 · 3.23 Impact Factor
  • Source
    • "some produces alterations in gene expression that minimize the fitness cost associated with plasmid carriage (Harr and Schlötterer, 2006; Navarre et al., 2006; Doyle et al., 2007; Shintani et al., 2010; Yun et al., 2010). An alternative explanation for the reduction in the cost of coexisting plasmids that we observed could be that plasmid gene expression decreases during co-infection. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Plasmids have a key role in the horizontal transfer of genes among bacteria. Although plasmids are catalysts for bacterial evolution, it is challenging to understand how they can persist in bacterial populations over the long term because of the burden they impose on their hosts (the 'plasmid paradox'). This paradox is especially perplexing in the case of 'small' plasmids, which are unable to self-transfer by conjugation. Here, for the first time, we investigate how interactions between co-infecting plasmids influence plasmid persistence. Using an experimental model system based on interactions between a diverse assemblage of 'large' plasmids and a single small plasmid, pNI105, in the pathogenic bacterium Pseudomonas aeruginosa, we demonstrate that positive epistasis minimizes the cost associated with carrying multiple plasmids over the short term and increases the stability of the small plasmid over a longer time scale. In support of these experimental data, bioinformatic analysis showed that associations between small and large plasmids are more common than would be expected owing to chance alone across a range of families of bacteria; more generally, we find that co-infection with multiple plasmids is more common than would be expected owing to chance across a wide range of bacterial phyla. Collectively, these results suggest that positive epistasis promotes plasmid stability in bacterial populations. These findings pave the way for future mechanistic studies aimed at elucidating the molecular mechanisms of plasmid-plasmid interaction, and evolutionary studies aimed at understanding how the coevolution of plasmids drives the spread of plasmid-encoded traits.The ISME Journal advance online publication, 24 October 2013; doi:10.1038/ismej.2013.182.
    The ISME Journal 10/2013; 8(3). DOI:10.1038/ismej.2013.182 · 9.30 Impact Factor
  • Source
    • "Bacterial chromosome organization is mediated by nucleoid-associated proteins (NAPs) (Wang et al., 2011). The specificity of NAP–DNA binding is determined by the differences in the GC content in specific regions of the DNA (Lucchini et al., 2006; Navarre et al., 2006; Castang et al., 2008; Smits and Grossman, 2010; Yun et al., 2010; Gordon et al., 2011). For example, the Salmonella NAP specifically binds to DNA regions with low GC content and inhibits expression of the genes present in these regions (Lucchini et al., 2006; Navarre et al., 2006). "
    Frontiers in Microbiology 12/2012; 3:420. DOI:10.3389/fmicb.2012.00420 · 3.99 Impact Factor
Show more