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Ken F. Jarrell - One of the best experts on this subject based on the ideXlab platform.

  • bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

  • Bypassing the need for the transcriptional activator eara through a spontaneous deletion in the BRE portion of the fla operon promoter in Methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    © 2017 Ding, Berezuk, Khursigara and Jarrell. In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (ΔearA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ΔearA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ΔearA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA may help recruit transcription factor B to a weak BRE in the fla promoter of wild-type cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

Yan Ding - One of the best experts on this subject based on the ideXlab platform.

  • bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

  • Bypassing the need for the transcriptional activator eara through a spontaneous deletion in the BRE portion of the fla operon promoter in Methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    © 2017 Ding, Berezuk, Khursigara and Jarrell. In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (ΔearA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ΔearA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ΔearA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA may help recruit transcription factor B to a weak BRE in the fla promoter of wild-type cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

Alison Berezuk - One of the best experts on this subject based on the ideXlab platform.

  • bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

  • Bypassing the need for the transcriptional activator eara through a spontaneous deletion in the BRE portion of the fla operon promoter in Methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    © 2017 Ding, Berezuk, Khursigara and Jarrell. In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (ΔearA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ΔearA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ΔearA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA may help recruit transcription factor B to a weak BRE in the fla promoter of wild-type cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

Cezar M Khursigara - One of the best experts on this subject based on the ideXlab platform.

  • bypassing the need for the transcriptional activator eara through a spontaneous deletion in the bre portion of the fla operon promoter in methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (∆earA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ∆earA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ∆earA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

  • Bypassing the need for the transcriptional activator eara through a spontaneous deletion in the BRE portion of the fla operon promoter in Methanococcus maripaludis
    Frontiers in Microbiology, 2017
    Co-Authors: Yan Ding, Alison Berezuk, Cezar M Khursigara, Ken F. Jarrell
    Abstract:

    © 2017 Ding, Berezuk, Khursigara and Jarrell. In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (ΔearA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ΔearA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three Adenines within a string of seven Adenines in the transcription factor B recognition element (BRE). When the three Adenine deletion in the BRE was regenerated in a stock culture of the ΔearA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three Adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA may help recruit transcription factor B to a weak BRE in the fla promoter of wild-type cells but is not required for transcription from the fla promoter with a strong BRE, as in the three Adenine deletion version in the spontaneous mutant.

Steven R Ahrendt - One of the best experts on this subject based on the ideXlab platform.

  • Widespread Adenine N6-methylation of active genes in fungi
    Nature Genetics, 2017
    Co-Authors: Stephen J Mondo, Richard O Dannebaum, Rita C Kuo, Katherine B Louie, Adam J Bewick, Kurt Labutti, Sajeet Haridas, Alan Kuo, Asaf Salamov, Steven R Ahrendt
    Abstract:

    N6-methyldeoxyAdenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes^ 1 , 2 , 3 , 4 , but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages^ 5 . Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all Adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated Adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes. Igor Grigoriev and colleagues perform single-molecule real-time sequencing on 16 diverse fungal species to evaluate levels of Adenine methylation (6mA). They find that almost 3% of all Adenines are methylated in early-diverging fungi, and they identify clusters of methylated Adenines that are enriched at transcription start sites of active genes.

  • widespread Adenine n6 methylation of active genes in fungi
    Nature Genetics, 2017
    Co-Authors: Stephen J Mondo, Richard O Dannebaum, Katherine B Louie, Adam J Bewick, Kurt Labutti, Sajeet Haridas, Asaf Salamov, Steven R Ahrendt, Benjamin P Bowen
    Abstract:

    N6-methyldeoxyAdenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all Adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated Adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.