Transcriptional heterogeneity of catabolic genes on the plasmid pCAR1 causes host-specific carbazole degradation.

To elucidate why plasmid-borne catabolic ability differs among host bacteria, we assessed the expression dynamics of the P promoter on the carbazole-degradative conjugative plasmid pCAR1 in KT2440(pCAR1) (hereafter, KTPC) and CA10. The P promoter regulates the transcription of both the and operons, which are responsible for converting carbazole into anthranilate and anthranilate into catechol, respectively. In the presence of anthranilate, transcription of the P promoter is induced by the AraC/XylS family regulator AntR, encoded on pCAR1.

Reconsideration of the previously classified incompatibility groups of plasmids, IncP-1 and IncP-11.

This study presents the reassessment of earlier published data with reference to the article published in Environmental Microbiology entitled 'IncP-type plasmids carrying genes for antibiotic resistance or aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains' by Lo et al. This correspondence clarifies misperceptions of plasmids classified under incompatibility (Inc) groups IncP-1 and IncP-11.

The α- and β-Subunit Boundary at the Stem of the Mushroom-Like αβ-Type Oxygenase Component of Rieske Non-Heme Iron Oxygenases Is the Rieske-Type Ferredoxin-Binding Site.

Cumene dioxygenase (CumDO) is an initial enzyme in the cumene degradation pathway of Pseudomonas fluorescens IP01 and is a Rieske non-heme iron oxygenase (RO) that comprises two electron transfer components (reductase [CumDO-R] and Rieske-type ferredoxin [CumDO-F]) and one catalytic component (αβ-type oxygenase [CumDO-O]). Catalysis is triggered by electrons that are transferred from NAD(P)H to CumDO-O by CumDO-R and CumDO-F. To investigate the binding mode between CumDO-F and CumDO-O and to identify the key CumDO-O amino acid residues for binding, we simulated docking between the CumDO-O crystal structure and predicted model of CumDO-F and identified two potential binding sites: one is at the side-wise site and the other is at the top-wise site in mushroom-like CumDO-O.

Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass.

Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e.

Physiological changes in Rhodococcus ruber S103 immobilized on biobooms using low-cost media enhance stress tolerance and crude oil-degrading activity.

For economic feasibility, sugarcane molasses (0.5%, w/v) containing KHPO (0.26%, w/v) and mature coconut water, low value byproducts, were used in cultivation of Rhodococcus ruber S103 for inoculum production and immobilization, respectively.

Rhizospheric plant-microbe synergistic interactions achieve efficient arsenic phytoextraction by Pteris vittata.

Phytoextraction is a cost-effective and eco-friendly technology to remove arsenic (As) from contaminated soil using plants and associated microorganisms. Pteris vittata is the most studied As hyperaccumulator, which effectively takes up inorganic arsenate via roots. Arsenic solubilization and speciation occur prior to plant absorption in the rhizosphere, which play a key role in As phytoextraction by P.

Incorporation of DNA to Bacterial Vesicles by in .

Membrane vesicles (MVs) are released by various prokaryotes and play a role in the delivery of various cell-cell interaction factors. Recent studies have determined that these vesicles are capable of functioning as mediators of horizontal gene transfer. Outer membrane vesicles (OMVs) are a type of MV that is released by Gram-negative bacteria and primarily composed of outer membrane and periplasm components; however, it remains largely unknown why DNA is contained within OMVs.

A toxin-antitoxin system confers stability to the IncP-7 plasmid pCAR1.

Toxin-antitoxin (TA) systems were initially discovered as plasmid addiction systems. Previously, our studies implied that the high stability of the IncP-7 plasmid pCAR1 in different Pseudomonas spp. hosts was due to the presence of a TA system on the plasmid.

The rice wound-inducible transcription factor RERJ1 sharing same signal transduction pathway with OsMYC2 is necessary for defense response to herbivory and bacterial blight.

This study describes biological functions of the bHLH transcription factor RERJ1 involved in the jasmonate response and the related defense-associated metabolic pathways in rice, with particular focus on deciphering the regulatory mechanisms underlying stress-induced volatile emission and herbivory resistance. RERJ1 is rapidly and drastically induced by wounding and jasmonate treatment but its biological function remains unknown as yet. Here we provide evidence of the biological function of RERJ1 in plant defense, specifically in response to herbivory and pathogen attack, and offer insights into the RERJ1-mediated regulation of metabolic pathways of specialized defense compounds, such as monoterpene linalool, in possible collaboration with OsMYC2-a well-known master regulator in jasmonate signaling.

Crystal structure of the ferredoxin reductase component of carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3.

Carbazole 1,9a-dioxygenase (CARDO), which consists of an oxygenase component and the electron-transport components ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R), is a Rieske nonheme iron oxygenase (RO). ROs are classified into five subclasses (IA, IB, IIA, IIB and III) based on their number of constituents and the nature of their redox centres. In this study, two types of crystal structure (type I and type II) were resolved of the class III CARDO-R from Janthinobacterium sp.

Deciphering OPDA Signaling Components in the Momilactone-Producing Moss .

Jasmonic acid (JA) and its biologically active form jasmonoyl-L-isoleucine (JA-Ile) regulate defense responses to various environmental stresses and developmental processes in plants. JA and JA-Ile are synthesized from α-linolenic acids derived from membrane lipids 12-oxo-phytodienoic acid (OPDA). In the presence of JA-Ile, the COI1 receptor physically interacts with JAZ repressors, leading to their degradation, resulting in the transcription of JA-responsive genes by MYC transcription factors.

Fluviispira sanaruensis sp., nov., Isolated from a Brackish Lake in Hamamatsu, Japan.

Strain RF1110005, which was isolated from brackish lake water sampled at Lake Sanaru in Japan as a "filterable" bacterial strain, was characterized as a novel species in the genus Fluviispira, family Silvanigrellaceae, order Silvanigrellales, the class Oligoflexia and the phylum Bdellovibrionota. Cells of RF1110005 were aerobic, Gram stain negative, and show a pleomorphic morphology of spiral, filamentous and rod shapes. Catalase reaction was positive.

Genome-wide screening of genes associated with momilactone B sensitivity in the fission yeast Schizosaccharomyces pombe.

Momilactone B is a natural product with dual biological activities, including antimicrobial and allelopathic properties, and plays a major role in plant chemical defense against competitive plants and pathogens. The pharmacological effects of momilactone B on mammalian cells have also been reported. However, little is known about the molecular and cellular mechanisms underlying its broad bioactivity.

A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2.

A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as -hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of -hydroxybenzoate and vanillate, are located on a 0.

Effects of environmental factors and coexisting substrates on PAH degradation and transcriptomic responses of the defined bacterial consortium OPK.

The present study showed that syntrophic associations in a defined bacterial consortium, named OPK, containing Mycolicibacterium strains PO1 and PO2, Novosphingobium pentaromativorans PY1 and Bacillus subtilis FW1, led to effective pyrene degradation over a wide range of pH values, temperatures and salinities, as well as in the presence of a second polycyclic aromatic hydrocarbon (PAH). Anthracene, phenanthrene or fluorene facilitated complete pyrene degradation within 9 days, while fluoranthene delayed pyrene degradation. Interestingly, fluoranthene degradation was enhanced in the presence of pyrene.

Oxygen concentration affects frequency and range of transconjugants for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1.

The frequency of transconjugants were compared for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1 under aerobic and anaerobic conditions. Filter mating assays were performed with one donor strain and one recipient strain using different donors of Pseudomonas and recipient strains, including Pseudomonas, Pantoea, and Buttiauxella. Under anaerobic condition, frequencies of transconjugants for both plasmids were 101-103-fold lower than those under aerobic condition regardless of whether aerobically or anaerobically grown donors and recipients were used.

Azoxystrobin amine: A novel azoxystrobin degradation product from Bacillus licheniformis strain TAB7.

Azoxystrobin (AZ) is a broad-spectrum synthetic fungicide widely used in agriculture globally. However, there are concerns about its fate and effects in the environment. It is reportedly transformed into azoxystrobin acid as a major metabolite by environmental microorganisms.

Light Response of KT2440 Mediated by Class II LitR, a Photosensor Homolog.

KT2440 retains three homologs (PplR1 to PplR3) of the LitR/CarH family, an adenosyl B-dependent light-sensitive MerR family transcriptional regulator. Transcriptome analysis revealed the existence of a number of photoinducible genes, including , (encoding DNA photolyase), (furan-containing fatty acid synthase), (GTP cyclohydrolase I), (cryptochrome-like protein), and multiple genes without annotated/known function. Transcriptional analysis by quantitative reverse transcription-PCR with knockout mutants of to showed that a triple knockout completely abolished the light-inducible transcription in , which indicates the occurrence of ternary regulation of PplR proteins.

A Novel Small RNA on the KT2440 Chromosome Is Involved in the Fitness Cost Imposed by IncP-1 Plasmid RP4.

Plasmids can provide advantageous traits to host bacteria, although they may impose a fitness cost. Chromosome-encoded factors are important for regulating the expression of genes on plasmids, and host chromosomes may differ in terms of their interactions with a given plasmid. Accordingly, differences in fitness cost loading and compensatory co-evolution may occur for various host chromosome/plasmid combinations.

H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1.

H-NS family proteins regulate the expression of many genes by preferably binding to AT-rich genomic regions and altering DNA topology. They are found in both bacterial chromosomes and plasmids, and plasmid-encoded H-NS family proteins have sometimes been suggested to act as a molecular backup of the chromosomally encoded ones. Pmr is an H-NS family protein encoded on the catabolic plasmid pCAR1, which belongs to incompatibility P-7 group.

Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants.

Momilactones are bioactive diterpenoids that contribute to plant defense against pathogens and allelopathic interactions between plants. Both cultivated and wild grass species of and (barnyard grass) produce momilactones using a biosynthetic gene cluster (BGC) in their genomes. The bryophyte (formerly ) also produces momilactones, and the bifunctional diterpene cyclase gene which is responsible for the production of the diterpene framework, has been characterized.

Complete Genome Sequence of sp. Strain S3, a Marine Clade Member Capable of Degrading Carbazole.

We determined the complete genome sequence of sp. strain S3, a marine carbazole degrader isolated from Tokyo Bay in Japan that carries genes for aerobic anoxygenic phototrophy. Strain S3 has a 4.