Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

Rapid degradation of the organophosphate pesticide - Chlorpyrifos by a novel strain of Pseudomonas nitroreducens AR-3

The indiscriminate use of pesticides leads to serious food safety and toxicity issues and threatens the environment and biodiversity. Pseudomonas nitroreducens AR-3 isolated from pesticide contaminated agricultural soil removed 97% of chlorpyrifos (CP) in just 8 h, in a mineral salt medium (MSM) containing glucose (1.0 g/L) and yeast extract (0.5 g/L) at 30 °C and 2% (v/v) inoculum when challenged with 100 mg/L CP. 3, 5, 6-trichloro 2-pyridinol (TCP), the degradation product of CP was detected only in low levels, indicating its further degradation. Organophosphate hydrolase (OPH), the enzyme considered responsible for CP degradation, had an intracellular localization. Crude OPH (1 mg/ml) removed 42% of 100 mg/L chlorpyrifos in just 2 h, indicating a rapid rate of degradation. Ultra-fast degradation of chlorpyrifos with an inducible OPH marks the potential of P. nitroreducens AR-3 for bioremediation of organophosphates. The strain AR-3 has the fastest rate of organophosphate degradation reported till date among Pseudomonads.

Optimized procedure of extraction, purification and proteomic analysis of nuclear proteins from mouse brain

BACKGROUND

The cell nucleus is a highly dynamic subcellular compartment performing crucial processes for functioning and administration of the cell. Proteomic analysis of isolated nuclear fraction enables in-depth insight into these processes leading to better understanding of physiological and pathological state of the brain. There is no universal method for nuclear proteome investigation and each biological material needs individual optimization. An additional difficulty is the large amount of nucleic acids, which impairs isoelectrofocusing of proteins and shotgun mass spectrometry analysis of complex peptide samples.

NEW METHOD

We performed the first comprehensive optimization of intact nuclei isolation from mouse brain in combination with nuclear protein purification prior to two-dimensional gel electrophoresis (2DE) and gel-free proteomic analysis.

RESULTS

Application of sonication, digestion with nuclease and protein precipitation with acetone allowed to obtain high quality 2DE gels. Shotgun mass spectrometry analysis of isolated proteins proved an enrichment in nuclear proteins. The 66.4% of 265 identified proteins had assigned nucleus localization in UniProt database. Gene Ontology analysis using DAVID platform revealed the highest fold enrichment in spliceosome (24.5), nuclear periphery (12.4) and nuclear matrix (11.3).

COMPARISON WITH EXISTING METHODS

The proposed procedure is tailored to mouse brain tissue nuclear subproteome investigation. The quality of isolated nuclei, the effectiveness of the protein purification, efficiency of protein recovery after precipitation and overall method reproducibility was taken into detailed consideration.

CONCLUSIONS

The elaborated procedure could be further applied for in-depth proteomic analysis of molecular processes occurring in the mouse brain nucleus.