Automated SPR-LC-MS/MS system for protein interaction analysis

We have developed a novel automated system to analyze protein complexes by integrating a surface plasmon resonance (SPR) biosensor with highly sensitive nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS). A His-tagged protein, which is also tagged with FLAG and biotinylated sequences, was expressed in mammalian cells. After purification by using the His tag from the cell lysate, the sample protein mixture was applied to an SPR biosensor and the protein complex was captured on the sensor chip. The automated SPR-LC-MS/MS was then performed: (1) two-step on-chip purification of the protein complex by using the FLAG and the biotinylated tags, (2) on-chip protease digestion of the complex, and (3) online nanoflow LC-MS/MS analysis of the resulting peptide fragments for protein identification. All of these processes could be monitored in real-time by the SPR biosensor. We validated the performance of the system using either FK506-binding protein 52 kDa (FKBP52) or ribosomal protein S19 (rpS19) as bait. Thus, the fully automated SPR-LC-MS/MS system appeared to be a powerful tool for functional proteomics studies, particularly for snapshot analysis of functional cellular complexes and machines.     

Identifying sea-run brown trout, Salmo trutta, using Sr : Ca ratios of otolith

 The migratory history of the brown trout, Salmo trutta, collected from Japanese rivers, was examined in terms of strontium (Sr) and calcium (Ca) uptake in the otolith, by means of wavelength dispersive X-ray spectrometry on an electron microprobe. Sea-run (anadromous) and freshwater-resident (nonanadromous) types of S. trutta were found to occur sympatrically. Otolith Sr concentration or Sr : Ca ratios of anadromous S. trutta fluctuated strongly along the life history transect in accordance with the migration (habitat) pattern from sea to freshwater. In contrast, the Sr concentration or the Sr : Ca ratios of nonanadromous fish remained at consistently low levels throughout the otolith. The higher ratios in anadromous S. trutta, in the otolith region from the core to 1500 μm, corresponded to the initial seagoing period, probably reflecting the ambient salinity or the seawater–freshwater gradient in Sr concentration. The findings clearly indicated that otolith Sr : Ca ratios reflected individual life histories, enabling the sea-run S. trutta to be distinguished from the freshwater-resident brown trout. Received: March 18, 2002 / Revised: May 15, 2002 / Accepted: June 5, 2002 Acknowledgments The authors are grateful to Messrs. T. Ikeda, S. Kudo, Y. Miyakoshi, M. Nagata, K. Shimoda, T. Takami, K. Takeuchi, and M. Ueda for their assistance in collecting specimens. This work was supported in part by Grant-in-Aid No. 13760138 from the Ministry of Education, Culture, Sports, Science and Technology, Japan. Correspondence to:Takaomi Arai     

Close linkage of human chromosomal pepsinogen A genes

We have obtained a clone containing two pepsinogen A genes in a single insert by screening a recombinant cosmid library for human genomic DNA. Restriction endonuclease mappings of this cloned DNA showed that these two genes are very similar, but distinct in structure, and that they are closely linked to one another in the human chromosome DNA. The close arrangement of the genes with very similar structures could facilitate the homologous recombination or the unequal crossing-over which accounts for high frequency of haplotype variation in copy number of pepsinogen A genes as reported by Taggart et al.     

Isolation of functional single cells from environments using a micromanipulator: application to study denitrifying bacteria

We developed a novel method to isolate functionally active single cells from environmental samples and named it the functional single-cell (FSC) isolation method. This method is based on a combination of substrate-responsive direct viable counts, live-cell staining with 5-carboxyfluorescein diacetate acetoxymethyl ester, and micromanipulation followed by cultivation in a medium. To evaluate this method, we applied it to study a denitrifying community in rice paddy soil. Similar denitrifier counts were obtained by the conventional most probable number analysis and our FSC isolation method. Using the FSC isolation method, 37 denitrifying bacteria were isolated, some of which harbored copper-containing nitrite reductase gene (nirK). The 16S rRNA gene analysis showed that members belonging to the genera Azospirillum and Ochrobactrum may be the major denitrifiers in the rice paddy soil. These results indicate that the FSC isolation method is a useful tool to obtain functionally active single cells from environmental samples.     

Streptococcal Sialidase I. Isolation and Properties of Sialidase Produced by Group K Streptococcus

A survey has been made of the activity of a wide variety of standard strains of streptococci against bovine submaxillary mucin. Strain 6646 (group K) and strain D 168A "X" (group M) completely broke down and strain H 60R (group F) incompletely broke down bound sialic acid of bovine submaxillary mucin added to the growth medium. Among these strains, strain 6646 (group K) produced sialidase in the cell and in the culture fluid. An appropriate amount of glucose in the culture medium stimulated growth and the production of enzyme, but an excess of glucose in the culture medium caused abundant growth without production of the enzyme. The streptococcal sialidase was precipitated from the culture fluid by ammonium sulfate at 50% saturation, and further purification was achieved by diethylaminoethyl cellulose chromatography. Ca(++) and Co(++) stimulated the sialidase activity, and Mn(++), Zn(++), and ethylenediaminetetraacetate inhibited it. With acetate buffer, the optimal pH lay between 5 and 6. Sialic acid was detected in the reaction product of the streptococcal sialidase and bovine submaxillary mucin.     

Phosphorylation-dependent interaction of kinesin light chain 2 and the 14-3-3 protein

The protein 14-3-3 is a key regulator in a cell signaling pathway mediated by protein phosphorylation. To identify the cellular targets of this protein systematically, we have employed a proteomic approach: protein components pulled down from PC12 cells stably expressing a myc-tagged 14-3-3eta isoform were analyzed by means of SDS-PAGE and mass spectrometry. This procedure allowed us to identify more than 30 proteins that include various known and unknown targets of the 14-3-3 protein. Among them are several proteins in the membrane traffic pathway, such as the heavy and light chains (KHC/KIF5B and KLC2) of conventional kinesin, a heterotetrameric mechanochemical motor involved in the ATP-dependent movement of vesicles and organelles along microtubules. Subsequent analysis showed that 14-3-3 directly binds to kinesin heterodimers through interaction with KLC2 and that this interaction is dependent on the phosphorylation of KLC2. Studies on the interaction between 14-3-3 and KLC2 variants expressed in cultured cells coupled with mass spectrometric analysis proved that Ser575 is the site of phosphorylation in KLC2 that is responsible for the in vivo interaction with the 14-3-3 protein. These data add KLC2 to the growing list of 14-3-3 targets, and suggest a role of 14-3-3 in the phosphorylation-regulated cellular transport of vesicles and organelles.     

Bacterial extracellular protease activities in field soils under different fertilizer managements

The major extracellular endopeptidase from Bacillus subtilis PF212 (isolated from paddy field soil) and B. subtilis CF80 (isolated from upland field soil) belongs to the group of serine proteases produced by Bacillus spp. known as subtilisins (optimum pH 7.0, optimum temperature 60 degrees C, and molecular mass 28 kDa). The NH2-terminal amino acid sequence (20 amino acids) of the endopeptidase from (i) strain CF80 was identical with that of subtilisin BPN' and (ii) strain PF212 was identical with that of subtilisin Amylosacchariticus. The properties (i.e., effect of inhibitors) of these endopeptidases were similar to those of the overall soil endopeptidase and soil endopeptidases extracted from paddy field soil. From the numbers of B. subtilis we isolated from paddy fields and found to produce a subtilisin-like serine protease, it seemed possible to consider that subtilisin was one of the soil endopeptidases in paddy field soils. The major extracellular endopeptidase from Serratia marcescens (strains 4-12-132, 4-12-131, and 4-60-110) isolated from upland field soils applied with animal slurry is a serratial metalloprotease (optimum pH 9.5, optimum temperature 40 degrees C, and molecular mass 50 kDa). The NH2-terminal amino acid sequence (20 amino acids) of the endopeptidase from strain 4-12-132 was identical with that of serratial metalloprotease, and partial DNA sequence of the endopeptidase gene of S. marcescens 4-12-132 had high homology with that of the serratial metalloprotease gene. The properties (i.e., effect of inhibitors) of this endopeptidase were similar to those of the overall soil endopeptidase in upland fields applied with animal slurry. Thus, it was possible to consider that serratial metalloprotease was one of the soil endopeptidases in upland fields applied with animal slurry.