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Yun Juan Chang - One of the best experts on this subject based on the ideXlab platform.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Matt Nolan, Alex CopelandAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Tijana Glavina Del Rio, Matt NolanAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Arpita Bose - One of the best experts on this subject based on the ideXlab platform.
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Genetic Redundancy in iron and manganese transport in the metabolically versatile bacterium rhodopseudomonas palustris tie 1
Applied and Environmental Microbiology, 2020Co-Authors: Rajesh Singh, Tahina Onina Ranaivoarisoa, Dinesh Gupta, Wei Bai, Arpita BoseAbstract:ABSTRACT The purple nonsulfur bacterium Rhodopseudomonas palustris TIE-1 can produce useful biochemicals such as bioplastics and biobutanol. Production of such biochemicals requires intracellular electron availability, which is governed by the availability and the transport of essential metals such as iron (Fe). Because of the distinct chemical properties of ferrous [Fe(II)] and ferric iron [Fe(III)], different systems are required for their transport and storage in bacteria. Although Fe(III) transport systems are well characterized, we know much less about Fe(II) transport systems except for the FeoAB system. Iron transporters can also import manganese (Mn). We studied Fe and Mn transport by five putative Fe transporters in TIE-1 under metal-replete, metal-depleted, oxic, and anoxic conditions. We observed that by overexpressing feoAB, efeU, and nramp1AB, the intracellular concentrations of Fe and Mn can be enhanced in TIE-1 under oxic and anoxic conditions, respectively. The deletion of a single gene/operon does not attenuate Fe or Mn uptake in TIE-1 regardless of the growth conditions used. This indicates that Genetically dissimilar yet functionally redundant Fe transporters in TIE-1 can complement each other. Relative gene expression analysis shows that feoAB and efeU are expressed during Fe and Mn depletion under both oxic and anoxic conditions. The promoters of these transporter genes contain a combination of Fur and Fnr boxes, suggesting that their expression is regulated by both Fe and oxygen availability. The findings from this study will help us modulate intracellular Fe and Mn concentrations, ultimately improving TIE-1’s ability to produce desirable biomolecules. IMPORTANCERhodopseudomonas palustris TIE-1 is a metabolically versatile bacterium that can use various electron donors, including Fe(II) and poised electrodes, for photoautotrophic growth. TIE-1 can produce useful biomolecules, such as biofuels and bioplastics, under various growth conditions. Production of such reduced biomolecules is controlled by intracellular electron availability, which, in turn, is mediated by various iron-containing proteins in the cell. Several putative Fe transporters exist in TIE-1’s genome. Some of these transporters can also transport Mn, part of several important cellular enzymes. Therefore, understanding the ability to transport and respond to various levels of Fe and Mn under different conditions is important to improve TIE-1’s ability to produce useful biomolecules. Our data suggest that by overexpressing Fe transporter genes via plasmid-based expression, we can increase the import of Fe and Mn in TIE-1. Future work will leverage these data to improve TIE-1 as an attractive microbial chassis and future biotechnological workhorse.
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Genetic Redundancy in iron and manganese transport in the metabolically versatile bacterium rhodopseudomonas palustris tie 1
bioRxiv, 2020Co-Authors: Rajesh Singh, Tahina Onina Ranaivoarisoa, Dinesh Gupta, Wei Bai, Arpita BoseAbstract:The purple non-sulfur bacterium Rhodopseudomonas palustris TIE-1 can produce useful biochemicals such as bioplastics and biobutanol. Production of such biochemicals requires intracellular electron availability, which is governed by the availability and the transport of essential metals such as iron (Fe). Because of the distinct chemical properties of ferrous [Fe(II)] and ferric iron [Fe(III)], different transport systems are required for their transport and storage in bacteria. Although Fe(III) transport systems are well characterized, we know much less about Fe(II) transport systems except for the FeoAB system. Iron transporters can also import manganese (Mn). Here, we study Fe and Mn transport by five putative Fe transporters in TIE-1 under metal-replete, -deplete, oxic and anoxic conditions. We observe that by overexpressing feoAB, efeU, and nramp1AB, the intracellular concentration of Fe and Mn can be enhanced in TIE-1, under oxic and anoxic conditions, respectively. The deletion of a single gene/operon does not attenuate Fe or Mn uptake in TIE-1 regardless of the growth conditions used. This indicates that Genetically dissimilar yet functionally redundant Fe transporters in TIE-1 can complement each other. Relative gene expression analysis shows that feoAB and efeU are expressed during Fe and Mn depletion under both oxic and anoxic conditions. The promoters of these transporter genes contain a combination of Fur and Fnr boxes suggesting that their expression is regulated by both Fe and oxygen availability. The findings from this study will help us modulate intracellular Fe and Mn concentration, ultimately improving TIE-19s ability to produce desirable biomolecules.
Olga Chertkov - One of the best experts on this subject based on the ideXlab platform.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Matt Nolan, Alex CopelandAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Tijana Glavina Del Rio, Matt NolanAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Loren Hauser - One of the best experts on this subject based on the ideXlab platform.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Matt Nolan, Alex CopelandAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Tijana Glavina Del Rio, Matt NolanAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Miriam Land - One of the best experts on this subject based on the ideXlab platform.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Matt Nolan, Alex CopelandAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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non contiguous finished genome sequence and contextual data of the filamentous soil bacterium ktedonobacter racemifer type strain sosp1 21t
Standards in Genomic Sciences, 2011Co-Authors: Yun Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Tijana Glavina Del Rio, Matt NolanAbstract:Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum ‘Chloroflexi’. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum ‘Chloroflexi’. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the Genetic Redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.