Recombinant Haemophilus influenzae Uncharacterized protein HI_1126 (HI_1126)

What is Haemophilus influenzae protein HI_1126?

HI_1126 is an uncharacterized protein from Haemophilus influenzae with conflicting UniProt identifiers (P44114 vs. O86234) across different databases. It lacks experimental validation regarding its specific biological function, though it remains a target of interest in H. influenzae research. The protein is primarily studied in recombinant form to enable structural and functional characterization efforts. Despite being part of the H. influenzae genome, which has been extensively sequenced and analyzed in over 10,000 isolates globally, HI_1126's specific role remains unclear in the context of this major opportunistic human pathogen .

What are the optimal storage conditions for recombinant HI_1126?

Recombinant HI_1126 demonstrates greatest stability when stored as follows:

Repeated freeze-thaw cycles significantly reduce protein activity and should be avoided. For optimal results, reconstitute lyophilized protein in sterile water at concentrations between 0.1-1.0 mg/mL with 5-50% glycerol as a stabilizing agent. When planning long-term experiments, it is advisable to prepare aliquots immediately after reconstitution to minimize freeze-thaw degradation.

How is HI_1126 conserved across different Haemophilus influenzae lineages?

While specific conservation data for HI_1126 is limited in the provided sources, H. influenzae generally shows a highly admixed population structure with low core genome nucleotide diversity and evidence of pervasive negative selection . Based on comparative genomic analyses of H. influenzae strains, we can infer:

Recent whole-genome sequencing of >4,000 isolates from northwestern Thailand combined with nearly 6,000 published genomes reveals significant genetic admixture across H. influenzae populations . This suggests that conservation of specific proteins like HI_1126 should be evaluated within the context of this dynamic genome structure, particularly in light of the high recombination rates observed in H. influenzae species (rho/theta values typically ranging from 0.58-1.6) .

What structural analysis techniques are most informative for HI_1126 characterization?

Multiple structural biology approaches can be employed for HI_1126 characterization, with complementary techniques yielding the most comprehensive structural insights:

Recombinant production of HI_1126 enables application of these techniques, particularly X-ray crystallography and NMR for high-resolution structure determination. For optimal results, protein sample preparation should include rigorous quality control (SDS-PAGE, mass spectrometry) to ensure sample homogeneity prior to structural analysis. When analyzing structural data, contextualizing findings within H. influenzae's genomic plasticity and population structure can provide additional evolutionary insights .

How can functional genomics approaches be applied to characterize HI_1126?

Functional genomics offers powerful tools for elucidating HI_1126's biological role through systematic approaches:

Transformation-based experimental evolution studies have proven particularly informative for H. influenzae research, with "transformed recombinant enrichment profiling" (TREP) allowing researchers to generate complex pools of recombinants, apply phenotypic selection, and use deep sequencing to identify genetic variations responsible for specific traits . This approach could be applied to investigate HI_1126's potential role in virulence, metabolism, or antibiotic resistance by comparing variant alleles across clinical isolates.

What proteomic approaches can identify HI_1126 interaction partners?

Several complementary proteomic methods can characterize the protein interaction network of HI_1126:

Immunoassays are available for antibody-based detection of HI_1126, which could facilitate co-immunoprecipitation studies. When designing interaction studies, researchers should consider H. influenzae's highly admixed population structure and variable expression patterns in different growth conditions or infection models . Integration of proteomic findings with transcriptomic data from H. influenzae in relevant host environments can provide contextual understanding of HI_1126 function.

How should researchers resolve the UniProt ID discrepancy for HI_1126?

The conflicting UniProt identifiers (P44114 vs. O86234) for HI_1126 require careful verification:

When reporting research on HI_1126, explicitly state which identifier was used and provide sequence information in supplementary materials to avoid confusion. The inconsistency highlights a broader challenge in H. influenzae research, where genomic plasticity, especially in non-typeable strains, complicates standardized nomenclature . This discrepancy exemplifies why cross-referencing with official databases is essential when working with uncharacterized proteins.

What expression systems yield optimal recombinant HI_1126 production?

Selection of an appropriate expression system significantly impacts recombinant HI_1126 quality and yield:

For bacterial expression, codon optimization based on the highly admixed nature of H. influenzae genomes should be considered . Given that H. influenzae shows low core genome nucleotide diversity and evidence of pervasive negative selection , expression constructs should be designed to account for selective pressures on codon usage. After expression, rigorous quality control including gel electrophoresis, mass spectrometry, and activity assays is essential before proceeding to structural or functional analyses.

What controls should be included when studying HI_1126 in vitro?

When designing functional assays, researchers should consider the genetic diversity observed in H. influenzae populations, particularly the highly admixed structure and evidence of recombination events . This diversity may influence the function of HI_1126 across different strains, necessitating testing in multiple genetic backgrounds. Additionally, controls for environmental conditions relevant to H. influenzae pathogenesis (e.g., oxygen limitation, nutrient restriction) may reveal condition-specific roles.

How does HI_1126 relate to H. influenzae virulence and pathogenesis?

While direct experimental evidence for HI_1126's role in pathogenesis is currently lacking, contextual analysis provides important research directions:

Comparative genomic analyses of H. influenzae strains have revealed that invasive disease capability is not restricted to specific subpopulations , suggesting that virulence factors like HI_1126 may function in diverse genetic backgrounds. Research shows that certain lineages harbor nearly pan-resistant characteristics , raising questions about whether HI_1126 might contribute to antimicrobial resistance mechanisms. Further investigation should consider the global establishment of multi-drug resistant lineages as an urgent research priority .

What bioinformatic approaches can predict HI_1126 function?

Computational methods can guide functional hypotheses for uncharacterized proteins like HI_1126:

When applying these methods to HI_1126, researchers should consider H. influenzae's highly admixed population structure and evidence of pervasive negative selection . The extensive recombination observed in H. influenzae genomes (with rho/theta values ranging from 0.58 to 1.6) suggests that gene neighborhood analysis should be interpreted cautiously, as genomic context may vary significantly between strains.

How might HI_1126 fit into H. influenzae metabolic networks?

Understanding metabolic context provides functional hypotheses for HI_1126:

Recent research identified a consistent pattern of gene replacement where the pxpB gene (encoding 5-oxoprolinase subunit) was replaced by a mobile cassette containing genes potentially involved in sugar metabolism across certain H. influenzae lineages . While not directly linked to HI_1126, this observation highlights the importance of investigating metabolic adaptations in H. influenzae. Metabolomic approaches have proven valuable for understanding H. influenzae adaptations to the human airway environment and could be applied to investigate HI_1126's metabolic context.

What novel approaches could accelerate functional characterization of HI_1126?

Emerging technologies offer promising avenues for HI_1126 functional elucidation:

Integration of these approaches with established methodologies like transformation-based experimental evolution could rapidly advance understanding of HI_1126. The highly admixed population structure of H. influenzae presents an opportunity to leverage natural genetic variation for functional studies through comparative genomics and transcriptomics across diverse isolates.

How can systems biology integrate HI_1126 into comprehensive H. influenzae models?

Systems-level integration provides holistic understanding of HI_1126 function:

Genomic, transcriptomic, proteomic, and metabolomic-based approaches have all contributed significantly to understanding H. influenzae interactions with human airways . These multi-omics approaches could be leveraged to position HI_1126 within the broader context of H. influenzae biology. The extensive whole-genome sequencing data available (>4,000 isolates from Thailand plus nearly 6,000 published genomes) provides a rich foundation for systems-level analyses incorporating evolutionary perspectives.

What implications might HI_1126 research have for understanding emerging multi-drug resistant H. influenzae?

Investigating HI_1126 in the context of antimicrobial resistance could yield valuable insights:

With increasing reports of multi-drug resistance in H. influenzae and the establishment of nearly pan-resistant lineages globally , understanding proteins like HI_1126 may contribute to addressing this urgent public health concern. Research should consider the potential role of HI_1126 in the context of highly admixed population structures and pervasive negative selection observed in H. influenzae , which may influence the evolution of resistance mechanisms.