Masaharu Kamo

Bacterial membranes: possible source of a major dissolved protein in seawater

Abstract We have measured dissolved protein at a variety of depths at three stations in the Pacific, ranging from the tropics to the subarctic. Most of the dissolved protein at these stations is distributed over a wide range of molecular masses, but consists of fewer than thirty individual proteins. One, with an apparent molecular mass of 48 kDa, is a major constituent at all stations. Its N-terminal amino acid sequence was found to be a homologue of porin P, a trans-outer-membrane channel protein of Gram-negative bacteria. Correspondence of N-terminal amino acid sequences and apparent molecular masses between this dissolved protein and porin P indicates that almost the complete homologue of porin P, from the N-terminus to (probably) the C-terminus, survives without modification in the water column. Persistence of appreciable amounts of an identifiable protein suggests a pathway for production of dissolved organic matter whereby enzyme-resistant biopolymers survive and accumulate in the sea.

Isolation and characterization of a Photosystem II complex from the red alga Cyanidium caldarium: association of cytochrome c-550 and a 12 kDa protein with the complex.

A Photosystem II (PS II) complex was purified from an acidophilic as well as a thermophilic red alga, Cyanidium caldarium. The purified PS II complex was essentially devoid of phycobiliproteins and other contaminating components, and showed a high oxygen-evolving activity of 2375 mumol O2/mg Chl per h using phenyl-p-benzoquinone as the electron acceptor. The expression of this high activity did not require addition of exogenous Ca2+, although EDTA reduced the activity by 40%. This effect of EDTA can be reversed not only by Ca2+ but also by Mg2+; a similar Mg2+ effect has been observed in purified cyanobacterial PS II but not in higher plant PS II. Immunoblotting analysis indicated the presence of major intrinsic polypeptides commonly found in PS II from cyanobacteria and higher plants as well as the extrinsic 33 kDa protein. Antibodies against the extrinsic 23 and 17 kDa proteins of higher plant PS II, however, did not crossreact with any polypeptides in the purified PS II, indicating the absence of these proteins in the red alga. In contrast, two other extrinsic proteins of 17 and 12 kDa were present in the red algal PS II; they were released by 1 M Tris or Urea/NaCl treatment but not by 1 M NaCl. The 17 kDa polypeptide was identified to be cytochrome c-550 from heme-staining, immunoblot analysis and N-terminal amino acid sequencing, and the 12 kDa protein was found to be homologous to the 12 kDa extrinsic protein of cyanobacterial PS II from its N-terminal sequence. These results indicate that PS II from the red alga is closely related to PS II from cyanobacteria rather than to that from higher plants, and that the replacement of PS II extrinsic cytochrome c-550 and the 12 kDa protein by the extrinsic 23 and 17 kDa proteins occurred during evolution from red algae to green algae and higher plants.

The mechanism of the degradation of psaB gene product, one of the photosynthetic reaction center subunits of photosystem I, upon photoinhibition

The psaB gene product (PsaB protein), one of the reaction center subunits of Photosystem I (PS I), was specifically degraded by light illumination of spinach thylakoid membranes. The degradation of the protein yielded N-terminal fragments of molecular mass 51 kDa and 45 kDa. The formation of the 51 kDa fragment was i) partially suppressed by the addition of phenylmethylsulfonyl fluoride or 3,4-dichloroisocoumarin, which are inhibitors of serine proteases, and ii) enhanced in the presence of hydrogen peroxide during photoinhibitory treatment, but iii) not detected following hydrogen peroxide treatment in the dark. These results suggest that the hydroxyl radical produced at the reduced iron-sulfur centers in PS I triggers the conformational change of the PS I complex, which allows access of a serine-type protease to PsaB. This results in the formation of the 51 kDa N-terminal fragment, presumably by cleavage on the loop exposed to the stromal side, between putative helices 8 and 9. On the other hand, the formation of the 45 kDa fragment, which was enhanced in the presence of methyl viologen but did not accompany the photoinhibition of PS I, was not affected by the addition of hydrogen peroxide or protease inhibitors. Another fragment of 18 kDa was identified as a C-terminal counterpart of the 45 kDa fragment. N-terminal sequence analysis of the 18 kDa fragment revealed that the cleavage occurred between Ala500 and Val501 on the loop exposed to the lumenal side, between putative helices 7 and 8 of the PsaB protein.

Proteome analysis of mouse brain: Two-dimensional electrophoresis profiles of tissue proteins during the course of aging

Mouse brain proteins were isolated from five regions (cerebellum, cerebral cortex, hippocampus, striatum, and cervical spinal cord) at five ages from the 10th week to the 24th month, and separated by two‐dimensional gel electrophoresis (2‐DE). 2‐DE was carried out with an immobilized pH gradient bar in the first dimension, and by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis in the second dimension. Over one thousand protein spots were visualized by silver staining and quantified by image processing. In the analyses, 58 protein spots were distinguishable among the above five brain regions, and 17 proteins were shown to be varied in quantity in the course of aging. Partial amino‐terminal sequences and/or internal sequences for a total of 301 protein spots were analyzed. One hundred and eighty proteins appeared to have blocked N‐termini and 122 proteins were identified. Twenty‐seven new proteins were identified by sequence homology search. A mouse brain proteome database was constructed, which consists of the 2‐DE map images and the respective spot data files with 15 related references.

Identification of Domains on the Extrinsic 33-kDa Protein Possibly Involved in Electrostatic Interaction with Photosystem II Complex by Means of Chemical Modification*

The extrinsic 33-kDa protein of photosystem II (PSII) was modified with various reagents, and the resulting proteins were checked for the ability to rebind to PSII and to reactivate oxygen evolution. While modification of more than eight carboxyl groups of aspartyl and glutamyl residues with glycine methyl ester did not affect the rebinding and reactivating capabilities, modification of amino groups of lysyl residues with either N-succinimidyl propionate or 2,4,6-trinitrobenzene sulfonic acid or modification of guanidino groups of arginyl residues with 2,3-butanedione resulted in a loss of rebinding and reactivating capabilities of the 33-kDa protein. Moreover, the number of lysyl and arginyl residues susceptible to modification was significantly decreased when the protein was bound to PSII as compared with when it was free in solution, whereas the number of carboxyl groups modified was little affected. These results suggested that positive charges are important for the electrostatic interaction between the extrinsic 33-kDa protein and PSII intrinsic proteins, whereas negative charges on the protein do not contribute to such interaction. By a combination of protease digestion and mass spectroscopic analysis, the domains of lysyl residues accessible to N-succinimidyl propionate or 2,4,6-trinitrobenzene sulfonic acid modification only when the 33-kDa protein is free in solution were determined to be Lys4, Lys20, Lys66-Lys76, Lys101, Lys105, Lys130, Lys159, Lys186, and Lys230-Lys236. These domains include those previously reported accessible to N-hydroxysuccinimidobiotin only in solution (Frankel and Bricker (1995) Biochemistry 34, 7492-7497), and may be important for the interaction of the 33-kDa protein with PSII intrinsic proteins.

Comparative analysis of brain proteins from p53-deficient mice by two-dimensional electrophoresis

p53 is a tumor suppressor protein that regulates many cellular processes including the cell cycle, DNA repair, and apoptosis. It also serves as a critical regulator of neuronal apoptosis in the central nervous system (CNS). To elucidate the role of p53 in the CNS, brain proteins of p53 knock‐out mice (p53−/−) were analyzed by two‐dimensional gel electrophoresis (2‐DE) and compared with those from p53 wild type (p53+/+) mice. Six types of brain tissue (temporal cortex, cerebellum, hippocampus, striatum, olfactory bulb, and cervical spinal cord) and other control tissues (lung and blood) from 18‐week‐old non‐stress‐induced mice were analyzed. The morphology of brains from p53−/− mice appeared to be normal and identical to that of p53+/+ mice, although lungs showed diffuse tumors that may have been caused by p53 deficiency. Comparative 2‐D gel analysis showed that, on average, 7 of 886 spots from brain tissue were p53−/− specific, whereas 12 of 1008 spots from lung tissue were p53−/− specific. N‐terminal amino acid sequence was determined for p53−/− specific proteins. In all brain tissues from p53−/− mice, a newly identified mouse mitochondrial NADH‐ubiquinone oxidoreductase 24 kDa subunit showed decreased expression, and apolipoprotein A1 acidic forms showed increased expression. In addition, brain‐type creatine kinase B chain and tubulin β‐5 N‐terminal fragment were increased in the p53−/− cerebellum, and a new protein in mouse, hydroxyacylglutathione hydrolase (glyoxalase II) was decreased in the temporal cortex of p53−/− mice. The alterations in protein expression identified in this study may imply a p53‐related brain function. This is the first proteomic analysis on the p53−/− mouse brain, and further information based on this study will provide new insights into the p53 function in the CNS.

Identification of domains on the 43 kDa chlorophyll-carrying protein (CP43) that are shielded from tryptic attack by binding of the extrinsic 33 kDa protein with Photosystem II complex

The structural association of the spinach 33 kDa extrinsic protein with the 43 kDa chlorophyll-carrying protein (CP43) in oxygen-evolving photosystem II (PS II) complexes was investigated by comparing the peptide mappings and N-terminal sequences of the trypsin-digested products of NaCl-washed PS II membranes, which bind the 33 kDa protein, with those of CaCl2-washed PS II membranes, which lack the 33 kDa protein. (1) Peptide from N-terminus to Arg26 of CP43, which is exposed to stromal side, was digested in both PS II membranes, independent of binding of the 33 kDa protein. (2) Peptide bond of Arg357-Phe358 located in the large extrinsic loop E of CP43, which is exposed to lumenal side, was cleaved by trypsin in CaCl2-washed PS II membranes but not in NaCl-washed PS II membranes. This indicates that the region around Arg357-Phe358 in loop E of CP43 is shielded from tryptic attack by binding of the 33 kDa protein to PS II. (3) Trypsin treatment of CaCl2-washed PS II membranes also cleaved peptide bond between Lys457 and Gly458 in C-terminal region of CP43, while no cleavage of this region was detected by trypsin treatment of NaCl-washed PS II membranes. This implies that a conformational change of the C-terminal region of CP43 which is exposed to stromal side occurred upon removal of the 33 kDa protein, which makes the C-terminal region accessible to trypsin. (4) Release of peptide from Gln60 to C-terminus of the alpha-subunit of cytochrome b-559 was detected only in trypsin treatment of CaCl2-washed PS II membranes, indicating that the C-terminal region of this subunit is shielded from tryptic attack by binding of the 33 kDa protein. (5) The PS II membranes, in which Arg357-Phe358, Lys457-Gly458 of CP43 and the C-terminal part of the cytochrome b-559 alpha-subunit had been cleaved by trypsin, was no longer able to bind the 33 kDa protein. This strongly suggests that a domain in loop E of CP43 and/or the C-terminal region of the cytochrome b-559 alpha-subunit are necessary for binding of the extrinsic 33 kDa protein to PS II.

Transforming growth factor-β1 induces epithelial-mesenchymal transition and integrin α3β1-mediated cell migration of HSC-4 human squamous cell carcinoma cells through Slug.

We investigated whether transforming growth factor (TGF)-β1 promoted epithelial-mesenchymal transition (EMT) and migration of human oral squamous cell carcinoma (hOSCC) cells. Among 6 hOSCC cell lines investigated, Smad2 phosphorylation and TGF-β target genes expression were most clearly upregulated following TGF-β1 stimulation in HSC-4 cells, indicating that HSC-4 cells were the most responsive to TGF-β1. In addition, the expression levels of the mesenchymal markers N-cadherin and vimentin were most clearly induced in HSC-4 cells among the hOSCC cell lines by TGF-β1 stimulation. Interestingly, E-cadherin and β-catenin at the cell surface were internalized in HSC-4 cells stimulated with TGF-β1. In addition, the expression levels of the EMT-related transcription factor Slug was significantly upregulated on TGF-β1 stimulation. Moreover, the downregulation of Slug by RNA interference clearly inhibited the TGF-β1-induced expression of mesenchymal marker and the migration of HSC-4 cells. Proteomics analysis also revealed that the expression levels of integrin α3β1-targeted proteins were upregulated in TGF-β1-stimulated HSC-4 cells. Neutral antibodies against integrin α3 and β1, as well as a focal adhesion kinase (FAK) inhibitor, clearly suppressed TGF-β1-induced cell migration. These results suggest that the EMT and integrin α3β1/FAK pathway-mediated migration of TGF-β1-stimulated HSC-4 hOSCC cells is positively controlled by Slug.

Application of chemical selective cleavage methods to analyze post-translational modification in proteins

Three chemical specific cleavage reactions, one for the carboxyl side of aspartyl peptide bonds, one for the carboxyl side of asparaginyl peptide bonds and another for the amino side of seryl/threonyl peptide bonds have been recently established. Additionally, these reactions simultaneously react on several post‐translationally modified groups in peptides or proteins. The modified groups cover the external modifications N‐formyl, N‐acetyl, N‐pyroglutamyi residues and C‐terminal‐α amide, as well as the internal modifications such as O‐acetyl serine, phosphorylated serine/tyrosine, sulfonylated tyrosine, glycosylated serine/threonine and glycosylated asparagine. These three cleavage reactions relate to key amino acids for modifications, deamidation for asparagine, phosphorylation and acetylation for serine, and glycosylation for asparagine, serine and threonine. The chemical reactions on these modifications change the peptide mapping pattern, and information from these reactions may contribute characterization and location of post‐translational modified groups in the protein.

Development of Novel C-Terminal Sequencing Methods

Development of a reliable C-terminal sequencing method has been expected from various aspects including sequencing protein, analyzing posttranslational process, confirming recombinant proteins and cloning. Carboxypeptidase digestion has been commonly used with limitations. Since a classical isothiocyanate degradation was proposed, several modifications were reported in the past two conferences (Hawkes and Boyd, 1991; Inglis et al., 1991; Miller and Shively, 1989). The present paper summarizes two related novel carboxy-terminal sequencing methods using perfluorinated carboxylic acids in monohydrate form and carboxylic acid anhydrides. These reagents produce the mixtures of C-terminal successive degraded molecules which are able to be analyzed by fast-atom-bombardment (FAB)- or electrospray ionization (ESI)-mass spectrometry (MS).