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The IHF regulon of exponentially growing Pseudomonas putida cells.

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Title: The IHF regulon of exponentially growing Pseudomonas putida cells.
Authors: Silva‐Rocha, Rafael1, Chavarría, Max1, Kleijn, Roelco J.2, Sauer, Uwe2, de Lorenzo, Víctor1
Source: Environmental Microbiology. Jan2013, Vol. 15 Issue 1, p49-63. 15p.
Subjects: Pseudomonas putida, Integration host factor, Bacterial cells, Cell growth, Bacterial metabolism, RNA polymerases, Cell culture, Bacterial gene mapping
Abstract: Integration host factor (IHF) sites are largely absent from intergenic regions of ORFs encoding central metabolic functions in Pseudomonas putida mt-2. To gain an insight into this unequal distribution of otherwise abundant IHF-binding sequences, the transcriptome of IHF-plus and IHF-minus cells growing exponentially on glucose as sole carbon source was examined. In parallel, the cognate metabolic fluxes of the wild-type P. putida strain and its ihfA derivative were determined by culturing cells to a steady-state physiological regime with 13C-labelled glucose. While expression of many transcripts was altered by the lack of IHF, flux balance analysis revealed that the ihfA mutation did not influence central carbon metabolism. Identification of multiple IHF sites adjacent to genes responsive to the factor allowed a refinement of the consensus and the mapping of the preferred binding positions for activation or repression of associated promoters. That few (if any) of the genes affected by IHF involved core pathways suggested that the central carbon metabolism tolerates the loss of the factor. Instead, IHF controlled various cell surface-related functions and downregulated genes encoding ribosomal proteins, the alpha subunit of RNA polymerase and components of the ATP synthase. These results were confirmed with lacZ fusions to a suite of promoters detected in the transcriptome as affected by IHF. Taken together, the data suggest that IHF plays a role in the physiological shift that sets P. putida for entering stationary phase. [ABSTRACT FROM AUTHOR]
Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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DbLabel: Engineering Source
An: 84578151
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  Data: The IHF regulon of exponentially growing Pseudomonas putida cells.
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  Data: <searchLink fieldCode="AR" term="%22Silva‐Rocha%2C+Rafael%22">Silva‐Rocha, Rafael</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Chavarría%2C+Max%22">Chavarría, Max</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Kleijn%2C+Roelco+J%2E%22">Kleijn, Roelco J.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Sauer%2C+Uwe%22">Sauer, Uwe</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22de+Lorenzo%2C+Víctor%22">de Lorenzo, Víctor</searchLink><relatesTo>1</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Environmental+Microbiology%22">Environmental Microbiology</searchLink>. Jan2013, Vol. 15 Issue 1, p49-63. 15p.
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  Data: <searchLink fieldCode="DE" term="%22Pseudomonas+putida%22">Pseudomonas putida</searchLink><br /><searchLink fieldCode="DE" term="%22Integration+host+factor%22">Integration host factor</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+cells%22">Bacterial cells</searchLink><br /><searchLink fieldCode="DE" term="%22Cell+growth%22">Cell growth</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+metabolism%22">Bacterial metabolism</searchLink><br /><searchLink fieldCode="DE" term="%22RNA+polymerases%22">RNA polymerases</searchLink><br /><searchLink fieldCode="DE" term="%22Cell+culture%22">Cell culture</searchLink><br /><searchLink fieldCode="DE" term="%22Bacterial+gene+mapping%22">Bacterial gene mapping</searchLink>
– Name: Abstract
  Label: Abstract
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  Data: Integration host factor (IHF) sites are largely absent from intergenic regions of ORFs encoding central metabolic functions in Pseudomonas putida mt-2. To gain an insight into this unequal distribution of otherwise abundant IHF-binding sequences, the transcriptome of IHF-plus and IHF-minus cells growing exponentially on glucose as sole carbon source was examined. In parallel, the cognate metabolic fluxes of the wild-type P. putida strain and its ihfA derivative were determined by culturing cells to a steady-state physiological regime with 13C-labelled glucose. While expression of many transcripts was altered by the lack of IHF, flux balance analysis revealed that the ihfA mutation did not influence central carbon metabolism. Identification of multiple IHF sites adjacent to genes responsive to the factor allowed a refinement of the consensus and the mapping of the preferred binding positions for activation or repression of associated promoters. That few (if any) of the genes affected by IHF involved core pathways suggested that the central carbon metabolism tolerates the loss of the factor. Instead, IHF controlled various cell surface-related functions and downregulated genes encoding ribosomal proteins, the alpha subunit of RNA polymerase and components of the ATP synthase. These results were confirmed with lacZ fusions to a suite of promoters detected in the transcriptome as affected by IHF. Taken together, the data suggest that IHF plays a role in the physiological shift that sets P. putida for entering stationary phase. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
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  Data: <i>Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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RecordInfo BibRecord:
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      – Type: doi
        Value: 10.1111/j.1462-2920.2012.02750.x
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      – Code: eng
        Text: English
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        PageCount: 15
        StartPage: 49
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      – SubjectFull: Pseudomonas putida
        Type: general
      – SubjectFull: Integration host factor
        Type: general
      – SubjectFull: Bacterial cells
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      – SubjectFull: Cell growth
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      – SubjectFull: Bacterial metabolism
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      – SubjectFull: RNA polymerases
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      – SubjectFull: Cell culture
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      – SubjectFull: Bacterial gene mapping
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      – TitleFull: The IHF regulon of exponentially growing Pseudomonas putida cells.
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            NameFull: Silva‐Rocha, Rafael
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            NameFull: Chavarría, Max
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            NameFull: Kleijn, Roelco J.
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            NameFull: Sauer, Uwe
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              Text: Jan2013
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