Haemophilus influenzae 2019
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PROVIDER: PRJNA175345 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome analysis of NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, and NTHi 86-028NPrpsL∆fur(pT-fur) strains Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts. Changes in gene expression patterns in response to host microenvironments are likely critical for survival. One such system of gene regulation is the ability to carefully regulate iron uptake. A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi. To understand the regulation of iron homeostasis in NTHi, fur was deleted in the NTHi strain 86-028NPrpsL. Using RNA-Seq, we identified both protein-encoding and small RNA genes whose expression was repressed or activated by Fur. Overall design: These data comprise transcriptional anaylses of an rpsL mutant of 86-028NP, an isogenic fur mutant of 86-028NPrpsL and a complemented fur mutant strain. All strains were grown in defined medium containing 10 µg/ml human hemoglobin to mid-log phase. Cells were then harvested and RNA extracted. A total of three biological replicates were generated for these analyses. Analysis of transcriptomes using the Illumina HiSeq 2000 of three strains of nontypeable Haemophilus influenzae which include NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, and NTHi 86-028NPrpsL∆fur(pT-fur) strains. For each strain three biological replicates were analyzed
2015-07-01 | E-GEOD-58890 | biostudies-arrayexpress
Project description:Schilling2000- Genome-scale metabolic network
of Haemophilus influenzae (iCS400)
This model is described in the article:
Assessment of the metabolic
capabilities of Haemophilus influenzae Rd through a
genome-scale pathway analysis.
Schilling CH, Palsson BO.
J. Theor. Biol. 2000 Apr; 203(3):
249-283
Abstract:
The annotated full DNA sequence is becoming available for a
growing number of organisms. This information along with
additional biochemical and strain-specific data can be used to
define metabolic genotypes and reconstruct cellular metabolic
networks. The first free-living organism for which the entire
genomic sequence was established was Haemophilus influenzae.
Its metabolic network is reconstructed herein and contains 461
reactions operating on 367 intracellular and 84 extracellular
metabolites. With the metabolic reaction network established,
it becomes necessary to determine its underlying pathway
structure as defined by the set of extreme pathways. The H.
influenzae metabolic network was subdivided into six subsystems
and the extreme pathways determined for each subsystem based on
stoichiometric, thermodynamic, and systems-specific
constraints. Positive linear combinations of these pathways can
be taken to determine the extreme pathways for the complete
system. Since these pathways span the capabilities of the full
system, they could be used to address a number of important
physiological questions. First, they were used to reconcile and
curate the sequence annotation by identifying reactions whose
function was not supported in any of the extreme pathways.
Second, they were used to predict gene products that should be
co-regulated and perhaps co-expressed. Third, they were used to
determine the composition of the minimal substrate requirements
needed to support the production of 51 required metabolic
products such as amino acids, nucleotides, phospholipids, etc.
Fourth, sets of critical gene deletions from core metabolism
were determined in the presence of the minimal substrate
conditions and in more complete conditions reflecting the
environmental niche of H. influenzae in the human host. In the
former case, 11 genes were determined to be critical while six
remained critical under the latter conditions. This study
represents an important milestone in theoretical biology,
namely the establishment of the first extreme pathway structure
of a whole genome.
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MODEL1507180053.
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2015-07-30 | MODEL1507180053 | BioModels
Project description:Whole-genome sequence of Haemophilus influenzae 2014-102
| PRJDB14741 | ENA