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  • American Society for Microbiology  (9)
  • 1
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 202, No. 20 ( 2020-09-23)
    Abstract: Pseudomonas putida KT2440 retains three homologs (PplR1 to PplR3) of the LitR/CarH family, an adenosyl B 12 -dependent light-sensitive MerR family transcriptional regulator. Transcriptome analysis revealed the existence of a number of photoinducible genes, including pplR1 , phrB (encoding DNA photolyase), ufaM (furan-containing fatty acid synthase), folE (GTP cyclohydrolase I), cryB (cryptochrome-like protein), and multiple genes without annotated/known function. Transcriptional analysis by quantitative reverse transcription-PCR with knockout mutants of pplR1 to pplR3 showed that a triple knockout completely abolished the light-inducible transcription in P. putida , which indicates the occurrence of ternary regulation of PplR proteins. A DNase I footprint assay showed that PplR1 protein specifically binds to the promoter regions of light-inducible genes, suggesting a consensus PplR1-binding direct repeat, 5′-T(G/A)TACAN 12 TGTA(C/T)A-3′. The disruption of B 12 biosynthesis cluster did not affect the light-inducible transcription; however, disruption of ppSB1-LOV (where LOV indicates “light, oxygen, or voltage”) and ppSB2-LOV , encoding blue light photoreceptors adjacently located to pplR3 and pplR2 , respectively, led to the complete loss of light-inducible transcription. Overall, the results suggest that the three PplRs and two PpSB-LOVs cooperatively regulate the light-inducible gene expression. The wide distribution of the pplR / ppSB-LOV cognate pair homologs in Pseudomonas spp. and related bacteria suggests that the response and adaptation to light are similarly regulated in the group of nonphototrophic bacteria. IMPORTANCE The LitR/CarH family is a new group of photosensor homologous to MerR-type transcriptional regulators. Proteins of this family are distributed to various nonphototrophic bacteria and grouped into at least five classes (I to V). Pseudomonas putida retaining three class II LitR proteins exhibited a genome-wide response to light. All three paralogs were functional and mediated photodependent activation of promoters directing the transcription of light-induced genes or operons. Two LOV (light, oxygen, or voltage) domain proteins, adjacently encoded by two litR genes, were also essential for the photodependent transcriptional control. Despite the difference in light-sensing mechanisms, the DNA binding consensus of class II LitR [T(G/A)TA(C/T)A] was the same as that of class I. This is the first study showing the actual involvement of class II LitR in light-induced transcription.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    American Society for Microbiology ; 2018
    In:  Journal of Bacteriology Vol. 200, No. 24 ( 2018-12-15)
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 200, No. 24 ( 2018-12-15)
    Abstract: The LitR/CarH protein family is an adenosyl B 12 (AdoB 12 )-dependent photoreceptor family with DNA-binding activity, and its homologs are widely distributed in the genomes of diverse bacterial genera. In this investigation, we studied the role and functions of a LitR homolog from a Gram-negative soil bacterium, Burkholderia multivorans , which does not possess an AdoB 12 -binding domain. Transcriptome analysis indicated the existence of 19 light-induced genes, including folE2 , cfaB , litS , photolyase gene phrB2 , and cryB , located in the region flanking litR . Disruption of litR caused constitutive expression of all the light-inducible genes, while mutation in the light-induced sigma factor gene, litS , abolished the transcription of the phrB2 operon and the cfa operon, indicating that LitR and LitS play a central role in light-inducible transcription. A gel shift assay showed that recombinant protein LitR specifically binds to the promoter regions of litR and the folE2 operon, and its binding was weakened by UV-A illumination. LitR absorbs light at maximally near 340 nm and exhibited a photocyclic response and light-dependent dissociation of multimer into tetramer. The litR mutant produced a 20-fold-higher intracellular level of folate than that of the wild-type strain. Thus, the evidence suggests that LitR light-dependently regulates the transcription of litR itself and the folE2 operon, resulting in the production of folate, and then the expressed RNA polymerase complex containing σ LitS directs the transcription of the phrB2 operon and the cfa operon. These light-dependent characteristics suggest that class III LitR, in complex with a UV-A-absorbing molecule, follows a novel light-sensing mechanism. IMPORTANCE Members of the LitR/CarH family are adenosyl B 12 -based photosensory transcriptional regulator involved in light-inducible carotenoid production in nonphototrophic bacteria. Our study provides the first evidence of the involvement of a class III LitR, which lacks an adenosyl B 12 -binding domain in the light response of Burkholderia multivorans belonging to betaproteobacteria. Our biochemical analysis suggests that class III LitR protein exhibits features as a photosensor including absorption of light at the UV-A region (λ max = ca. 340 nm), photocyclic response, and light-dependent dissociation. This suggests that class III LitR associates with a UV-A-absorbing molecule, and it has a photosensing mechanism distinguishable from that of the B 12 -based type.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 3
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 197, No. 14 ( 2015-07-15), p. 2301-2315
    Abstract: The LitR/CarH family of proteins is a light-sensitive MerR family of transcriptional regulators that contain an adenosyl B 12 (coenzyme B 12 or AdoB 12 )-binding domain at the C terminus. The genes encoding these proteins are found in phylogenetically diverse bacterial genera; however, the biochemical properties of these proteins from Gram-positive bacteria remain poorly understood. We performed genetic and biochemical analyses of a homolog of the LitR protein from Bacillus megaterium QM B1551, a Gram-positive endospore-forming soil bacterium. Carotenoid production was induced by illumination in this bacterium. In vivo analysis demonstrated that LitR plays a central role in light-inducible carotenoid production and serves as a negative regulator of the light-inducible transcription of crt and litR itself. Biochemical evidence showed that LitR in complex with AdoB 12 binds to the promoter regions of litR and the crt operon in a light-sensitive manner. In vitro transcription experiments demonstrated that AdoB 12 -LitR inhibited the specific transcription of the crt promoter generated by a σ A -containing RNA polymerase holoenzyme under dark conditions. Collectively, these data indicate that the AdoB 12 -LitR complex serves as a photoreceptor with DNA-binding activity in B. megaterium QM B1551 and that its function as a transcriptional repressor is fundamental to the light-induced carotenoid production. IMPORTANCE Members of the LitR/CarH family are AdoB 12 -based photosensors involved in light-inducible carotenoid production in nonphototrophic Gram-negative bacteria. Our study revealed that Bacillus LitR in complex with AdoB 12 also serves as a transcriptional regulator with a photosensory function, which indicates that the LitR/CarH family is generally involved in the light-inducible carotenoid production of nonphototrophic bacteria.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2015
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    American Society for Microbiology ; 2016
    In:  Genome Announcements Vol. 4, No. 4 ( 2016-08-25)
    In: Genome Announcements, American Society for Microbiology, Vol. 4, No. 4 ( 2016-08-25)
    Abstract: We report here the genome sequence of Filimonas lacunae , a bacterium of the family Chitinophagaceae characterized by high-CO 2 -dependent growth. The 7.81-Mb circular genome harbors many genes involved in carbohydrate degradation and related genetic regulation, suggesting the role of the bacterium as a carbohydrate degrader in diverse environments.
    Type of Medium: Online Resource
    ISSN: 2169-8287
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2016
    detail.hit.zdb_id: 2968655-6
    detail.hit.zdb_id: 2704277-7
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  • 5
    Online Resource
    Online Resource
    American Society for Microbiology ; 2008
    In:  Applied and Environmental Microbiology Vol. 74, No. 14 ( 2008-07-15), p. 4535-4538
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 74, No. 14 ( 2008-07-15), p. 4535-4538
    Abstract: Although some bacteria require an atmosphere with high CO 2 levels for their growth, CO 2 is not generally supplied to conventional screening cultures. Here, we isolated 84 bacterial strains exhibiting high-CO 2 dependence. Their phylogenetic affiliations imply that high-CO 2 culture has potential as an effective method to isolate unknown microorganisms.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    RVK:
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2008
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
    In: Genome Announcements, American Society for Microbiology, Vol. 4, No. 5 ( 2016-10-27)
    Abstract: Here, we report the draft genome sequence of Thermogemmatispora onikobensis NBRC 111776 T , an aerial mycelium- and spore-forming thermophilic bacterium belonging to the class Ktedonobacteria . The genome contains five biosynthetic gene clusters coding for secondary metabolites, such as terpene, thiopeptide, lantipeptide, nonribosomal peptide, and lassopeptide, suggesting the potential to produce secondary metabolites.
    Type of Medium: Online Resource
    ISSN: 2169-8287
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2016
    detail.hit.zdb_id: 2968655-6
    detail.hit.zdb_id: 2704277-7
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  • 7
    Online Resource
    Online Resource
    American Society for Microbiology ; 2005
    In:  Journal of Bacteriology Vol. 187, No. 1 ( 2005-01), p. 135-142
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 187, No. 1 ( 2005-01), p. 135-142
    Abstract: The amf gene cluster encodes a probable secretion system for a peptidic morphogen, AmfS, which induces aerial mycelium formation in Streptomyces griseus . Here we examined the transcriptional control mechanism for the promoter preceding amfT (P amfT ) directing the transcription of the amfTSBA operon. High-resolution S1 analysis mapped a transcriptional start point at 31 nucleotides upstream of the translational start codon of amfT . Low-resolution analysis showed that P amfT is developmentally regulated in the wild type and completely abolished in an amfR mutant. The −35 region of P amfT contained the consensus sequence for the binding of BldD, a pleiotropic negative regulator for morphological and physiological development in Streptomyces coelicolor A3(2). The cloned bldD locus of S. griseus showed high sequence similarity to the S. coelicolor counterpart. Transcription of bldD occurred constitutively in both the wild type and an A-factor-deficient mutant of S. griseus , which suggests that the regulatory role of BldD is independent of A-factor. The gel retardation assay revealed that purified BldD and AmfR recombinant proteins specifically bind P amfT . Overproduction of BldD in the wild-type cell conferred a bald phenotype (defective in aerial growth and streptomycin production) and caused marked repression of P amfT activity. An amfT -depleted mutant also showed a bald phenotype but P amfT activity was not affected. Both the bldD -overproducing wild-type strain and the amfT mutant were unable to induce aerial growth of an amfS mutant in a cross-feeding assay, which indicates that these strains are defective in the production of an active AmfS peptide. The results overall suggests that two independent regulators, AmfR and BldD, control P amfT activity via direct binding to determine the transcriptional level of the amf operon responsible for the production and secretion of AmfS peptide, which induces the erection of aerial hyphae in S. griseus .
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2005
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 8
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 187, No. 5 ( 2005-03), p. 1825-1832
    Abstract: Carotenoids are produced by a variety of organisms, but the mechanisms that regulate gene expression leading to carotenoid biosynthesis have been characterized for only a few organisms. In this study, we found that Streptomyces coelicolor A3(2), a gram-positive filamentous bacterium, produces carotenoids under blue light induction. The carotenoid fraction isolated from the cell extract contained multiple compounds, including isorenieratene and β-carotene. The carotenoid biosynthesis gene cluster of S. coelicolor consists of two convergent operons, crtEIBV and crtYTU , as previously shown for Streptomyces griseus . The crtEIBV null mutant completely lost its ability to produce carotenoids. The crt gene cluster is flanked by a regulatory region that consists of two divergent operons, litRQ and litSAB . The lit (light-induced transcription) genes encode a MerR-type transcriptional regulator (LitR), a possible oxidoreductase (LitQ), an extracytoplasmic function sigma factor (σ LitS ), a putative lipoprotein (LitA), and a putative anti-sigma factor (LitB). S1 protection assay revealed that the promoters preceding crtE (P crtE ), crtY (P crtY ), litR (P litR ), and litS (P litS ) are activated upon illumination. A litS mutant lost both the ability to produce carotenoids and the activities of P crtE , P crtY , and P litS , which suggested that σ LitS directs light-induced transcription from these promoters. An RNA polymerase holocomplex containing purified σ LitS recombinant protein generated specific P crtE and P crtY transcripts in an in vitro runoff transcriptional assay. A litR mutant that had an insertion of the kanamycin resistance gene was defective both in the ability to produce carotenoids and in all of the light-dependent promoter activities. Overexpression of litS resulted in constitutive carotenoid production in both the wild type and the litR mutant. These results indicate that σ LitS acts as a light-induced sigma factor that directs transcription of the crt biosynthesis gene cluster, whose activity is controlled by an unknown LitR function. This is the first report to describe light-inducible gene expression in Streptomyces .
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2005
    detail.hit.zdb_id: 1481988-0
    SSG: 12
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  • 9
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 193, No. 10 ( 2011-05-15), p. 2451-2459
    Abstract: Members of the CarA/LitR family are MerR-type transcriptional regulators that contain a C-terminal cobalamin-binding domain. They are thought to be involved in light-induced transcriptional regulation in a wide variety of nonphototrophic bacteria. Based on the distribution of this kind of regulator, the current study examined carotenoid production in Thermus thermophilus , and it was found to occur in a light-induced manner. litR and carotenoid and cobalamin biosynthesis genes were all located on the large plasmid of this organism. litR or cobalamin biosynthesis gene knockout mutants were unable to switch off carotenoid production under dark conditions, while a mutant with a mutation in the downstream gene adjacent to litR (TT_P0055), which encodes a CRP/FNR family transcriptional regulator, was unable to produce carotenoids, irrespective of light conditions. Overall, genetic and biochemical evidence indicates that LitR is bound by cobalamin and associates with the intergenic promoter region between litR and crtB (phytoene synthase gene), repressing the bidirectional transcription of litR and crtB . It is probable that derepression of LitR caused by some photodependent mechanism induces the expression of TT_P0055 protein, which serves as a transcriptional activator for the crtB operon and hence causes the expression of carotenoid biosynthesis and the DNA repair system under light condition.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2011
    detail.hit.zdb_id: 1481988-0
    SSG: 12
    Location Call Number Limitation Availability
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