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Subrata K Das - One of the best experts on this subject based on the ideXlab platform.

  • draft genome sequence of Marinomonas fungiae strain an44t jcm 18476t isolated from the coral fungia echinata from the andaman sea
    Genome Announcements, 2018
    Co-Authors: Prabla Kumari, Jhasketan Badhai, Subrata K Das
    Abstract:

    ABSTRACT Marinomonas fungiae strain AN44T was isolated from mucus of the coral Fungia echinata. Optimum growth occurs at 3 to 5% NaCl. The draft genome is 4.2 Mb, with 3,776 protein-coding genes. It harbors genes for the degradation of aromatic compounds, such as quinate, ferulate, p-coumarate, protocatechuate, and p-hydroxyphenylacetate.

  • Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104.
    Frontiers in microbiology, 2016
    Co-Authors: Jhasketan Badhai, Subrata K Das
    Abstract:

    The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5’-end of the typical host prfC gene, while ICEMfuInd1a was inserted at 5’-end of the atypical hipA-like gene. Despite their coexisting, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their common evolution from SXT-like ancestors. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE in M. fungiae due to mutations. Our analysis showed the presence of 16, 25 and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b and ICEMprChn1 respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hotspot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICEMprChn1 from M. profundimaris. Finally, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.

  • characterization of three novel sxt r391 integrating conjugative elements icemfuind1a and icemfuind1b and icemprchn1 identified in the genomes of Marinomonas fungiae jcm 18476t and Marinomonas profundimaris strain d104
    Frontiers in Microbiology, 2016
    Co-Authors: Jhasketan Badhai, Subrata K Das
    Abstract:

    The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5’-end of the typical host prfC gene, while ICEMfuInd1a was inserted at 5’-end of the atypical hipA-like gene. Despite their coexisting, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their common evolution from SXT-like ancestors. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE in M. fungiae due to mutations. Our analysis showed the presence of 16, 25 and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b and ICEMprChn1 respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hotspot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICEMprChn1 from M. profundimaris. Finally, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.

  • Marinomonas fungiae sp nov isolated from the coral fungia echinata from the andaman sea
    International Journal of Systematic and Evolutionary Microbiology, 2014
    Co-Authors: Prabla Kumari, Abhijit Poddar, Subrata K Das
    Abstract:

    A novel aerobic marine bacterium, strain AN44T, was isolated from the coral Fungia echinata sampled from the Andaman Sea, India. Cells were Gram-negative, motile and rod-shaped. Oxidase and catalase tests were positive. Heterotrophic growth was observed at pH 5.5–10 and at 16–42 °C, with optimum growth at pH 7–8 and 28 °C. Strain AN44T grew in the presence of 0.5–11 % (w/v) NaCl; the optimal NaCl concentration for growth was 3–5 %. The DNA G+C content was 47.8 mol%. Predominant cellular fatty acids of strain AN44T were C18 : 1ω7c, C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C10 : 0 3-OH, C12 : 0, C10 : 0, C14 : 0 and C18 : 0. The sole isoprenoid ubiquinone was Q-8. The polar lipids were an unidentified phospholipid, an unidentified aminophospholipid and two unidentified glycolipids. 16S rRNA gene sequence comparisons revealed that strain AN44T clustered within the radiation of the genus Marinomonas and showed similarity of 97.9 % with Marinomonas ostreistagni UST010306-043T, 97.8 % with Marinomonas aquimarina 11SM4T, 97.1 % with Marinomonas brasilensis R-40503T and 97.0 % with Marinomonas communis 8T. However, DNA–DNA relatedness between strain AN44T and closely related type strains was well below 70 %. On the basis of the data from the present polyphasic taxonomic study, strain AN44T is considered to represent a novel species of the genus Marinomonas , for which the name Marinomonas fungiae sp. nov. is proposed. The type strain is AN44T ( = JCM 18476T = LMG 27065T).

Antonio Sanchezamat - One of the best experts on this subject based on the ideXlab platform.

  • direct crispr spacer acquisition from rna by a natural reverse transcriptase cas1 fusion protein
    Science, 2016
    Co-Authors: Sukrit Silas, Antonio Sanchezamat, Georg Mohr, David J Sidote, Laura M Markham, Devaki Bhaya, Alan M Lambowitz, Andrew Fire
    Abstract:

    CRISPR systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats in type I and II CRISPR systems by the acquisition of short segments of DNA (spacers) from invasive elements. In several type III CRISPR systems, Cas1 is naturally fused to a reverse transcriptase (RT). In the marine bacterium Marinomonas mediterranea (MMB-1), we showed that a RT-Cas1 fusion protein enables the acquisition of RNA spacers in vivo in a RT-dependent manner. In vitro, the MMB-1 RT-Cas1 and Cas2 proteins catalyze the ligation of RNA segments into the CRISPR array, which is followed by reverse transcription. These observations outline a host-mediated mechanism for reverse information flow from RNA to DNA.

  • identification in Marinomonas mediterranea of a novel quinoprotein with glycine oxidase activity
    MicrobiologyOpen, 2013
    Co-Authors: Jonatan C Campillobrocal, Patricia Lucaselio, Antonio Sanchezamat
    Abstract:

    A novel enzyme with lysine-epsilon oxidase activity was previously described in the marine bacterium Marinomonas mediterranea. This enzyme differs from other l-amino acid oxidases in not being a flavoprotein but containing a quinone cofactor. It is encoded by an operon with two genes lodA and lodB. The first one codes for the oxidase, while the second one encodes a protein required for the expression of the former. Genome sequencing of M. mediterranea has revealed that it contains two additional operons encoding proteins with sequence similarity to LodA. In this study, it is shown that the product of one of such genes, Marme_1655, encodes a protein with glycine oxidase activity. This activity shows important differences in terms of substrate range and sensitivity to inhibitors to other glycine oxidases previously described which are flavoproteins synthesized by Bacillus. The results presented in this study indicate that the products of the genes with different degrees of similarity to lodA detected in bacterial genomes could constitute a reservoir of different oxidases.

  • Marinomonas alcarazii sp nov m rhizomae sp nov m foliarum sp nov m posidonica sp nov and m aquiplantarum sp nov isolated from the microbiota of the seagrass posidonia oceanica
    International Journal of Systematic and Evolutionary Microbiology, 2011
    Co-Authors: Patricia Lucaselio, Ester Marconoales, Elena Espinosa, Monica Ordax, Neus Garciasbonet, Nuria Marba, Carlos M. Duarte, Maria M. Lopez, Antonio Sanchezamat
    Abstract:

    Five novel Gram-reaction-negative aerobic marine bacterial strains with DNA G+C contents <50 mol% were isolated from the seagrass Posidonia oceanica. 16S rRNA sequence analysis indicated that they belonged to the genus Marinomonas. Major fatty acid compositions, comprising C10 : 0 3-OH, C16 : 0, C16 : 1ω7c and C18 : 1ω7c, supported the affiliation of these strains to the genus Marinomonas. Strains IVIA-Po-14bT, IVIA-Po-145T and IVIA-Po-155T were closely related to Marinomonas pontica 46-16T, according to phylogenetic analysis. However, DNA–DNA hybridization values <35 % among these strains revealed that they represented different species. Further differences in the phenotypes and minor fatty acid compositions were also found among the strains. Another two strains, designated IVIA-Po-181T and IVIA-Po-159T, were found to be closely related to M. dokdonensis DSW10-10T but DNA–DNA relatedness levels <40 % in pairwise comparisons, as well as some additional differences in phenotypes and fatty acid compositions supported the creation of two novel species. Accordingly, strains IVIA-Po-14bT ( = CECT 7730T  = NCIMB 14671T), IVIA-Po-145T ( = CECT 7377T  = NCIMB 14431T), IVIA-Po-155T ( = CECT 7731T  = NCIMB 14672T), IVIA-Po-181T ( = CECT 7376T  = NCIMB 14433T) and IVIA-Po-159T ( = CECT 7732T  = NCIMB 14673T) represent novel species, for which the names Marinomonas alcarazii sp. nov., Marinomonas rhizomae sp. nov., Marinomonas foliarum sp. nov., Marinomonas posidonica sp. nov. and Marinomonas aquiplantarum sp. nov. are proposed, respectively.

  • taxonomic study of Marinomonas strains isolated from the seagrass posidonia oceanica with descriptions of Marinomonas balearica sp nov and Marinomonas pollencensis sp nov
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Elena Espinosa, Patricia Lucaselio, Ester Marconoales, Monica Ordax, Neus Garciasbonet, Carlos M. Duarte, Daniel Gomez, Antonio Sanchezamat
    Abstract:

    Novel aerobic, Gram-negative bacteria with DNA G+C contents below 50 mol% were isolated from the culturable microbiota associated with the Mediterranean seagrass Posidonia oceanica. 16S rRNA gene sequence analyses revealed that they belong to the genus Marinomonas. Strain IVIA-Po-186 is a strain of the species Marinomonas mediterranea, showing 99.77 % 16S rRNA gene sequence similarity with the type strain, MMB-1(T), and sharing all phenotypic characteristics studied. This is the first description of this species forming part of the microbiota of a marine plant. A second strain, designated IVIA-Po-101(T), was closely related to M. mediterranea based on phylogenetic studies. However, it differed in characteristics such as melanin synthesis and tyrosinase, laccase and antimicrobial activities. In addition, strain IVIA-Po-101(T) was auxotrophic and unable to use acetate. IVIA-Po-101(T) shared 97.86 % 16S rRNA gene sequence similarity with M. mediterranea MMB-1(T), but the level of DNA-DNA relatedness between the two strains was only 10.3 %. On the basis of these data, strain IVIA-Po-101(T) is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas balearica sp. nov. is proposed. The type strain is IVIA-Po-101(T) (=CECT 7378(T) =NCIMB 14432(T)). A third novel strain, IVIA-Po-185(T), was phylogenetically distant from all recognized Marinomonas species. It shared the highest 16S rRNA gene sequence similarity (97.4 %) with the type strain of Marinomonas pontica, but the level of DNA-DNA relatedness between the two strains was only 14.5 %. A differential chemotaxonomic marker of this strain in the genus Marinomonas is the presence of the fatty acid C(17 : 0) cyclo. Strain IVIA-Po-185(T) is thus considered to represent a second novel species of the genus, for which the name Marinomonas pollencensis sp. nov. is proposed. The type strain is IVIA-Po-185(T) (=CECT 7375(T) =NCIMB 14435(T)). An emended description of the genus Marinomonas is given based on the description of these two novel species, as well as other Marinomonas species described after the original description of the genus.

  • alkali and halide resistant catalysis by the multipotent oxidase from Marinomonas mediterranea
    Journal of Biotechnology, 2005
    Co-Authors: Nuria Jimenezjuarez, Antonio Sanchezamat, Rosa Romanmiranda, Alejandro Valle Baeza, Rafael Vazquezduhalt, Brenda Valderrama
    Abstract:

    The incorporation of fungal laccases into novel applications has been delayed mainly due to their intrinsic sensitivity towards halides and alkaline conditions. In order to explore new sources of enzymes we evaluated the multipotent polyphenol oxidase PPO1 from the marine bacterium Marinomonas mediterranea. Here we report that, in contrast to its fungal counterparts, PPO1 remained functional above neutral pH presenting high specificity for phenolic compounds, in particular for methoxyl-substituted mono-phenols and catechols. These properties, in addition to its tolerance towards chloride (up to 1 M) and its elevated redox potential at neutral pH (0.9 V), suggest this enzyme may be an interesting candidate for specific applications such as the Amperometric determination of phenolic compounds and bio-fuel cells.

Patricia Lucaselio - One of the best experts on this subject based on the ideXlab platform.

  • identification in Marinomonas mediterranea of a novel quinoprotein with glycine oxidase activity
    MicrobiologyOpen, 2013
    Co-Authors: Jonatan C Campillobrocal, Patricia Lucaselio, Antonio Sanchezamat
    Abstract:

    A novel enzyme with lysine-epsilon oxidase activity was previously described in the marine bacterium Marinomonas mediterranea. This enzyme differs from other l-amino acid oxidases in not being a flavoprotein but containing a quinone cofactor. It is encoded by an operon with two genes lodA and lodB. The first one codes for the oxidase, while the second one encodes a protein required for the expression of the former. Genome sequencing of M. mediterranea has revealed that it contains two additional operons encoding proteins with sequence similarity to LodA. In this study, it is shown that the product of one of such genes, Marme_1655, encodes a protein with glycine oxidase activity. This activity shows important differences in terms of substrate range and sensitivity to inhibitors to other glycine oxidases previously described which are flavoproteins synthesized by Bacillus. The results presented in this study indicate that the products of the genes with different degrees of similarity to lodA detected in bacterial genomes could constitute a reservoir of different oxidases.

  • complete genome sequence of Marinomonas posidonica type strain ivia po 181t
    Standards in Genomic Sciences, 2012
    Co-Authors: Patricia Lucaselio, Lynne Goodwin, Tanja Woyke, Sam Pitluck, Matt Nolan, Janine C. Detter, Nikos C Kyrpides, Alex Copeland, David Bruce
    Abstract:

    Marinomonas posidonica IVIA-Po-181T Lucas-Elio et al. 2011 belongs to the family Oceanospirillaceae within the phylum Proteobacteria. Different species of the genus Marinomonas can be readily isolated from the seagrass Posidonia oceanica. M. posidonica is among the most abundant species of the genus detected in the cultured microbiota of P. oceanica suggesting a close relationship with this plant, which has a great ecological value in the Mediterranean Sea, covering an estimated surface of 38,000 Km2. Here we describe the genomic features of M. posidonica. The 3,899,940 bp long genome harbors 3,544 protein-coding genes and 107 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  • complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain mmb 1t
    Standards in Genomic Sciences, 2012
    Co-Authors: Patricia Lucaselio, Lynne Goodwin, Tanja Woyke, Sam Pitluck, Matt Nolan, Janine C. Detter, Nikos C Kyrpides, Alex Copeland, Hazuki Teshima
    Abstract:

    Marinomonas mediterranea MMB-1T Solano & Sanchez-Amat 1999 belongs to the family Oceanospirillaceae within the phylum Proteobacteria. This species is of interest because it is the only species described in the genus Marinomonas to date that can synthesize melanin pigments, which is mediated by the activity of a tyrosinase. M. mediterranea expresses other oxidases of biotechnological interest, such as a multicopper oxidase with laccase activity and a novel L-lysine-epsilon-oxidase. The 4,684,316 bp long genome harbors 4,228 protein-coding genes and 98 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  • Marinomonas alcarazii sp nov m rhizomae sp nov m foliarum sp nov m posidonica sp nov and m aquiplantarum sp nov isolated from the microbiota of the seagrass posidonia oceanica
    International Journal of Systematic and Evolutionary Microbiology, 2011
    Co-Authors: Patricia Lucaselio, Ester Marconoales, Elena Espinosa, Monica Ordax, Neus Garciasbonet, Nuria Marba, Carlos M. Duarte, Maria M. Lopez, Antonio Sanchezamat
    Abstract:

    Five novel Gram-reaction-negative aerobic marine bacterial strains with DNA G+C contents <50 mol% were isolated from the seagrass Posidonia oceanica. 16S rRNA sequence analysis indicated that they belonged to the genus Marinomonas. Major fatty acid compositions, comprising C10 : 0 3-OH, C16 : 0, C16 : 1ω7c and C18 : 1ω7c, supported the affiliation of these strains to the genus Marinomonas. Strains IVIA-Po-14bT, IVIA-Po-145T and IVIA-Po-155T were closely related to Marinomonas pontica 46-16T, according to phylogenetic analysis. However, DNA–DNA hybridization values <35 % among these strains revealed that they represented different species. Further differences in the phenotypes and minor fatty acid compositions were also found among the strains. Another two strains, designated IVIA-Po-181T and IVIA-Po-159T, were found to be closely related to M. dokdonensis DSW10-10T but DNA–DNA relatedness levels <40 % in pairwise comparisons, as well as some additional differences in phenotypes and fatty acid compositions supported the creation of two novel species. Accordingly, strains IVIA-Po-14bT ( = CECT 7730T  = NCIMB 14671T), IVIA-Po-145T ( = CECT 7377T  = NCIMB 14431T), IVIA-Po-155T ( = CECT 7731T  = NCIMB 14672T), IVIA-Po-181T ( = CECT 7376T  = NCIMB 14433T) and IVIA-Po-159T ( = CECT 7732T  = NCIMB 14673T) represent novel species, for which the names Marinomonas alcarazii sp. nov., Marinomonas rhizomae sp. nov., Marinomonas foliarum sp. nov., Marinomonas posidonica sp. nov. and Marinomonas aquiplantarum sp. nov. are proposed, respectively.

  • taxonomic study of Marinomonas strains isolated from the seagrass posidonia oceanica with descriptions of Marinomonas balearica sp nov and Marinomonas pollencensis sp nov
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Elena Espinosa, Patricia Lucaselio, Ester Marconoales, Monica Ordax, Neus Garciasbonet, Carlos M. Duarte, Daniel Gomez, Antonio Sanchezamat
    Abstract:

    Novel aerobic, Gram-negative bacteria with DNA G+C contents below 50 mol% were isolated from the culturable microbiota associated with the Mediterranean seagrass Posidonia oceanica. 16S rRNA gene sequence analyses revealed that they belong to the genus Marinomonas. Strain IVIA-Po-186 is a strain of the species Marinomonas mediterranea, showing 99.77 % 16S rRNA gene sequence similarity with the type strain, MMB-1(T), and sharing all phenotypic characteristics studied. This is the first description of this species forming part of the microbiota of a marine plant. A second strain, designated IVIA-Po-101(T), was closely related to M. mediterranea based on phylogenetic studies. However, it differed in characteristics such as melanin synthesis and tyrosinase, laccase and antimicrobial activities. In addition, strain IVIA-Po-101(T) was auxotrophic and unable to use acetate. IVIA-Po-101(T) shared 97.86 % 16S rRNA gene sequence similarity with M. mediterranea MMB-1(T), but the level of DNA-DNA relatedness between the two strains was only 10.3 %. On the basis of these data, strain IVIA-Po-101(T) is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas balearica sp. nov. is proposed. The type strain is IVIA-Po-101(T) (=CECT 7378(T) =NCIMB 14432(T)). A third novel strain, IVIA-Po-185(T), was phylogenetically distant from all recognized Marinomonas species. It shared the highest 16S rRNA gene sequence similarity (97.4 %) with the type strain of Marinomonas pontica, but the level of DNA-DNA relatedness between the two strains was only 14.5 %. A differential chemotaxonomic marker of this strain in the genus Marinomonas is the presence of the fatty acid C(17 : 0) cyclo. Strain IVIA-Po-185(T) is thus considered to represent a second novel species of the genus, for which the name Marinomonas pollencensis sp. nov. is proposed. The type strain is IVIA-Po-185(T) (=CECT 7375(T) =NCIMB 14435(T)). An emended description of the genus Marinomonas is given based on the description of these two novel species, as well as other Marinomonas species described after the original description of the genus.

Jhasketan Badhai - One of the best experts on this subject based on the ideXlab platform.

  • draft genome sequence of Marinomonas fungiae strain an44t jcm 18476t isolated from the coral fungia echinata from the andaman sea
    Genome Announcements, 2018
    Co-Authors: Prabla Kumari, Jhasketan Badhai, Subrata K Das
    Abstract:

    ABSTRACT Marinomonas fungiae strain AN44T was isolated from mucus of the coral Fungia echinata. Optimum growth occurs at 3 to 5% NaCl. The draft genome is 4.2 Mb, with 3,776 protein-coding genes. It harbors genes for the degradation of aromatic compounds, such as quinate, ferulate, p-coumarate, protocatechuate, and p-hydroxyphenylacetate.

  • Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104.
    Frontiers in microbiology, 2016
    Co-Authors: Jhasketan Badhai, Subrata K Das
    Abstract:

    The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5’-end of the typical host prfC gene, while ICEMfuInd1a was inserted at 5’-end of the atypical hipA-like gene. Despite their coexisting, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their common evolution from SXT-like ancestors. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE in M. fungiae due to mutations. Our analysis showed the presence of 16, 25 and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b and ICEMprChn1 respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hotspot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICEMprChn1 from M. profundimaris. Finally, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.

  • characterization of three novel sxt r391 integrating conjugative elements icemfuind1a and icemfuind1b and icemprchn1 identified in the genomes of Marinomonas fungiae jcm 18476t and Marinomonas profundimaris strain d104
    Frontiers in Microbiology, 2016
    Co-Authors: Jhasketan Badhai, Subrata K Das
    Abstract:

    The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5’-end of the typical host prfC gene, while ICEMfuInd1a was inserted at 5’-end of the atypical hipA-like gene. Despite their coexisting, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their common evolution from SXT-like ancestors. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE in M. fungiae due to mutations. Our analysis showed the presence of 16, 25 and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b and ICEMprChn1 respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hotspot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICEMprChn1 from M. profundimaris. Finally, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.

Francisco Solano - One of the best experts on this subject based on the ideXlab platform.

  • identification of an operon involved in tyrosinase activity and melanin synthesis in Marinomonas mediterranea
    Gene, 2004
    Co-Authors: Daniel Lopezserrano, Francisco Solano, Antonio Sanchezamat
    Abstract:

    The genomic region of Marinomonas mediterranea containing the genes required for tyrosinase activity and melanin synthesis has been cloned by marker rescue using the transposon-generated, amelanogenic strain T105. Five ORFs, two incomplete and three complete, have been sequenced in the genomic region where the transposon was inserted. RT-PCR analysis indicates that ORF 3, coding for tyrosinase, and ORF4, coding for a protein of 250 amino acids, are in the same transcriptional unit, constituting an operon whose promoter region has been determined by 5'-RACE. This operon has been sequenced in the wild-type and several mutant strains, indicating that both ORFs are required for expression of tyrosinase activity and melanin synthesis. The nitrosoguanidine generated, amelanogenic mutant ng56, shows a nonsense mutation in ORF3 coding for the tyrosinase. On the other hand, in the strain T105 the transposon is inserted in ORF4. The product of this gene is related to copper metabolism, since the addition of this metal ion to cell extracts or culture media partially restores melanin synthesis and tyrosinase activity in the strain T105. However, it does not show significant sequence similarity to previously characterized metallochaperones and hence may be an example of a new kind of those proteins. The operon has been denoted as ppoB, taking into consideration that ppoA denotes the M. mediterranea gene coding for the previously cloned polyphenol oxidase with laccase activity. This is the first demonstration of the tyrosinase gene forming part of an operon in a Gram-negative bacterium.

  • Marinomonas mediterranea is a lysogenic bacterium that synthesizes r bodies
    Microbiology, 2003
    Co-Authors: Diana Hernandezromero, Patricia Lucaselio, Francisco Solano, Daniel Lopezserrano, Antonio Sanchezamat
    Abstract:

    The melanogenic marine bacterium Marinomonas mediterranea synthesizes R-bodies as revealed by transmission electron microscopy. These structures were previously described in some obligate symbionts of paramecia and some free-living bacteria, none of which was isolated from sea water. In other micro-organisms, the synthesis of R-bodies has been related to extrachromosomal elements. Accordingly, M. mediterranea induction by mitomycin C or UV radiation resulted in the production of defective phages resembling bacteriocins, indicating that it is a lysogenic bacterium. Two mitomycin-C-resistant strains defective in prophage replication have been isolated. These mutants, and the previously obtained strains ngC1, T102 and T103, the latter mutated in the ppoS gene encoding a sensor histidine kinase, are affected not only in phage replication but also in polyphenol oxidase activities and melanin synthesis, suggesting a relationship between the control of all these processes.

  • regulation of polyphenol oxidase activities and melanin synthesis in Marinomonas mediterranea identification of ppos a gene encoding a sensor histidine kinasea
    Microbiology, 2002
    Co-Authors: Patricia Lucaselio, Francisco Solano, Antonio Sanchezamat
    Abstract:

    Marinomonas mediterranea is a melanogenic marine bacterium that expresses two different polyphenol oxidases. One of them is a multipotent laccase able to oxidize a wide range of substrates. The second enzyme is an SDS-activated tyrosinase. Using transposon mutagenesis, a mutant affected in the regulation of both polyphenol oxidase activities and melanogenesis has been isolated. The sequencing of the gene disrupted by the mini-Tn10 transposon in this mutant indicates that it encodes a hybrid sensor kinase. This sensor kinase shows three phosphorylated conserved domains: the transmitter domain containing a histidine site typical of sensor kinases, a receiver domain with an aspartate residue and an additional phosphotransferase domain with a second conserved histidine. This structural organization is characteristic of kinases participating in a phosphorelay system. Northern blot and lacZ operon fusions indicate that the multipotent laccase activity is regulated not only by PpoS but also by growth phase at the transcriptional level. These results suggest that PPO activities and melanin synthesis play a role in the adaptive response of M. mediterranea to stressful environmental conditions.

  • cloning and molecular characterization of a sds activated tyrosinase from Marinomonas mediterranea
    Pigment Cell Research, 2002
    Co-Authors: Daniel Lopezserrano, Antonio Sanchezamat, Francisco Solano
    Abstract:

    The sequence of the tyrosinase gene cloned from Marinomonas mediterranea is reported. It is the second tyrosinase cloned from a Gram negative bacterium. Its size is higher than that of Gram positive tyrosinases from Streptomyces, and more similar to the eukaryotic enzymes. Its sequence shares the features of copper-binding sites found in all tyrosinases. Based in the comparison of tyrosinases from all types of organisms, an extension of the characteristic signatures existing at Prosite is proposed. This tyrosinase shares with some plant and amphibian tyrosinases a strong specific activation by submicellar concentrations of SDS. Intrinsic fluorescence and kinetic properties indicate that the activation is caused by an SDS-dependent conformational change that facilitates the substrate accessibility to the dicopper active site.

  • dimethoxyphenol oxidase activity of different microbial blue multicopper proteins
    Fems Microbiology Letters, 2001
    Co-Authors: Francisco Solano, Patricia Lucaselio, Daniel Lopezserrano, Eva Maria Rubio Fernandez, Antonio Sanchezamat
    Abstract:

    2,6-Dimethoxyphenol is a versatile substrate for Pyricularia oryzae laccase, PpoA from Marinomonas mediterranea, phenoxazinone synthase from Streptomyces antibioticus and mammalian ceruloplasmin. In addition, in cellular extracts of microorganisms expressing other blue multicopper proteins with no enzymatic activity previously described, such as Escherichia coli (copper resistance CueO), Pseudomonas syringae and Xanthomonas campestris (copper resistance CopA), Bacillus subtilis (sporulation protein CotA) and Saccharomyces cerevisiae (iron transporter Fet3p), laccase activity is detected under appropriate conditions. This oxidase activity can be spectrophotometrically followed by the oxidation of 2,6-dimethoxyphenol. Specific staining after SDS–PAGE is also possible for some of these proteins. This detection assay can facilitate the study of the multiple functions that such proteins seem to carry out in a variety of microorganisms.