Nucleoid-associated proteins encoded on plasmids: Occurrence and mode of function

Shintani, Masaki; Suzuki-Minakuchi, Chiho; Nojiri, Hideaki

doi:10.1016/j.plasmid.2015.04.008

Cited by 45 publications

(35 citation statements)

References 107 publications

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“…The other MvaT proteins, especially TurE, might also play an important role(s) in such cooperation. In addition, pCAR1 carries two other NAP genes, phu and pnd, which encode a histone-like protein and an NdpA-like protein, respectively (14,15,19). Further in-depth analyses of the relationships between H-NS family proteins and these other NAP genes are required to understand the transcriptional cross talk between plasmids and the host cell chromosome.…”

Section: Relationships Between Dna-binding Regions Of Mvat Proteins Amentioning

confidence: 99%

“…Interestingly, genes encoding H-NS family proteins are also found in conjugative plasmids (14)(15)(16), and their products have a stealth function by silencing transcriptional perturbation of the host chromosome with minimal effects on host fitness (17,18). The IncP-7 carbazole-degradative plasmid pCAR1 was isolated from Pseudomonas resinovorans CA10 (19) and has been sequenced fully and found to carry an mvaT-homologous gene, pmr.…”

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confidence: 99%

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MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently

Yun

Takahashi

Shintani

et al. 2016

Appl Environ Microbiol

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dMvaT proteins are members of the H-NS family of proteins in pseudomonads. The IncP-7 conjugative plasmid pCAR1 carries an mvaT-homologous gene, pmr. In Pseudomonas putida KT2440 bearing pCAR1, pmr and the chromosomally carried homologous genes, turA and turB, are transcribed at high levels, and Pmr interacts with TurA and TurB in vitro. In the present study, we clarified how the three MvaT proteins regulate the transcriptome of P. putida KT2440(pCAR1). Analyses performed by a modified chromatin immunoprecipitation assay with microarray technology (ChIP-chip) suggested that the binding regions of Pmr, TurA, and TurB in the P. putida KT2440(pCAR1) genome are almost identical; nevertheless, transcriptomic analyses using mutants with deletions of the genes encoding the MvaT proteins during the log and early stationary growth phases clearly suggested that their regulons were different. Indeed, significant regulon dissimilarity was found between Pmr and the other two proteins. Transcription of a larger number of genes was affected by Pmr deletion during early stationary phase than during log phase, suggesting that Pmr ameliorates the effects of pCAR1 on host fitness more effectively during the early stationary phase. Alternatively, the similarity of the TurA and TurB regulons implied that they might play complementary roles as global transcriptional regulators in response to plasmid carriage.

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Section: Relationships Between Dna-binding Regions Of Mvat Proteins Amentioning

confidence: 99%

mentioning

confidence: 99%

MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently

Yun

Takahashi

Shintani

et al. 2016

Appl Environ Microbiol

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“…Moreover, a gene encoding an H-NS histone family homolog was adjacent to acr and anti-RM loci in a Moraxella catarrhalis plasmid (Figure 5b(iii)). MGE-encoded H-NS-like proteins are often considered "stealth proteins" that tamper with host gene expression (Shintani, Suzuki-Minakuchi and Nojiri, 2015;Vial and Hommais, 2019). Given the H-NS-mediated silencing of CRISPR-Cas adaptive immunity in E. coli (Pul et al, 2010;Westra et al, 2010), the lateral acquisition of H-NS homologs may help MGEs evade adaptive immunity, as previously proposed for certain plasmids (Dorman, 2014;Dorman and Ní Bhriain, 2020) and phages (Skennerton et al, 2011).…”

Section: Acrs Cluster With Anti-rm and Other Anti-defense Genesmentioning

confidence: 95%

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

Pinilla‐Redondo

Shehreen

Marino

et al. 2020

Preprint

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Many prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have evolved Anti-CRISPR (Acr) proteins to bypass this immunity, yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we uncover 11 new type I anti-CRISPR genes encoded on numerous chromosomal and extrachromosomal mobile genetic elements within Enterobacteriaceae and Pseudomonas. Candidate genes were identified adjacent to anti-CRISPR associated gene 5 (aca5) and assayed against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas), revealing the type I-F and/or I-E acr genes and a new aca (aca9). We find that acr genes not only associate with other acr genes, but also with inhibitors of distinct bacterial defense systems. These genomic regions appear to be "anti-defense islands", reminiscent of the clustered arrangement of "defense islands" in prokaryotic genomes. Our findings expand on the diversity of CRISPR-Cas inhibitors and reveal the potential exploitation of acr loci neighborhoods for identifying new anti-defense systems.

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“…Recently, it was shown that pCAR1 carries three genes encoding nucleoid‐associated proteins (NAPs): plasmid‐encoded MvaT‐like regulator [Pmr; ORF70 ( pmr )], plasmid‐encoded NdpA‐like protein [Pnd; ORF93 ( pnd )], and plasmid‐encoded HU‐like protein [Phu; ORF95a ( phu )] (Takeda et al ., ; Nojiri, ; Shintani et al ., ). NAPs compact bacterial DNA to form topological domain structures and are believed to influence transcription (Dillon and Dorman, ).…”

Section: Introductionmentioning

confidence: 97%

Effects of carbazole‐degradative plasmid pCAR1 on biofilm morphology in Pseudomonas putida KT2440

Lee

Takahashi

Oura

et al. 2016

Environ Microbiol Rep

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Bacteria typically form biofilms under natural conditions. To elucidate the effect of the carriage of carbazole-degradative plasmid pCAR1 on biofilm formation by host bacteria, we compared the biofilm morphology, using confocal laser scanning microscopy, of three pCAR1-free and pCAR1-carrying Pseudomonas hosts: P. putida KT2440, P. aeruginosa PAO1 and P. fluorescens Pf0-1. Although pCAR1 did not significantly affect biofilm formation by PAO1 or Pf0-1, pCAR1-carrying KT2440 became filamentous and formed flat biofilms, whereas pCAR1-free KT2440 formed mushroom-like biofilms. pCAR1 contains three genes encoding nucleoid-associated proteins (NAPs), namely, Pmr, Pnd and Phu. The enhanced filamentous morphology was observed in two double mutants [KT2440(pCAR1ΔpmrΔpnd) and KT2440(pCAR1ΔpmrΔphu)], suggesting that these NAPs are involved in modulating the filamentous phenotype. Transcriptome analyses of the double mutants identified 32 candidate genes that may be involved in filamentation of KT2440. Overexpression of PP_2193 in KT2440 induced filamentation and overexpression of PP_0308 or PP_0309 in KT2440(pCAR1) enhanced filamentation of cells over time. This suggests that pCAR1 induces development of an abnormal filamentous morphology by KT2440 via a process involving overexpression of several genes, such as PP_2193. In addition, pCAR1-encoded NAPs partly suppress too much filamentation of KT2440(pCAR1) by repressing transcription of some genes, such as PP_0308 and PP_0309.

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Nucleoid-associated proteins encoded on plasmids: Occurrence and mode of function

Cited by 45 publications

References 107 publications

MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently

MvaT Family Proteins Encoded on IncP-7 Plasmid pCAR1 and the Host Chromosome Regulate the Host Transcriptome Cooperatively but Differently

Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements

Effects of carbazole‐degradative plasmid pCAR1 on biofilm morphology in Pseudomonas putida KT2440

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