Purification of an Abf2p-like protein from mitochondrial nucleoids of yeast <Emphasis Type="Italic">Pichia jadinii</Emphasis> and its role in the packaging of mitochondrial DNA

A 26-kDa protein with highly basic pI was purified from the mitochondrial (mt-) nucleoids of the yeast Pichia jadinii by a combination of acid extraction, hydroxyapatite chromatography and DNA-cellulose chromatography. The 26-kDa protein has the ability to introduce a supercoil into circular plasmid DNA in the presence of topoisomerase I and to package mtDNA into nucleoid-like aggregates. The mt-nucleoids isolated from P. jadinii cells were disassembled in the presence of 2 M NaCl and reassembled into nucleoid-like aggregates by the removal of the salts. During the course of the reassembly of the mt-nucleoids, three specific proteins of 20 kDa, 26 kDa and 56 kDa predominantly precipitated after the centrifugation of the reassembled mt-nucleoids. These results suggest that the 26-kDa protein of P. jadinii has a similar function in the packaging of mtDNA to Abf2p, a major mitochondrial DNA-binding protein in Saccharomyces cerevisiae.     

Isolation and Characterization of Mitochondrial Nucleoids from the Yeast Pichia jadinii

Mitochondrial (mt) nucleoids were isolated with a high degreeof purity from the yeast Pichia jadinii, in which the mitochondrialDNA (mtDNA) is linear. Field-inversion gel electrophoresis (FIGE)revealed that significant amounts of mtDNA could be isolatedintact, as linear molecules of 41 kbp, from the isolated mt-nucleoids.Fifteen different proteins were detected in the mt-nucleoidfraction and, eight of these proteins bound to DNA. The patternsof mt-nucleoid proteins and of the DNA-binding proteins aftergel electrophoresis in the presence of SDS were somewhat differentfrom those of such proteins from Saccharomyces cerevisiae. Thecorresponding proteins isolated from the mt-nucleoids of fourother species of yeast in the genera Pichia and Williopsis alsodiffered from one another in terms of electrophoretic mobilityin the presence of SDS. In immunoblotting experiments, antibodiesthat had been raised against the 67-kDa protein of mt-nucleoidsfrom S. cerevisiae and the YMN-1 monoclonal antibody that isspecific for a 48-kDa protein in the mt-nucleoids from S. cerevisiaedid not recognize any proteins in the mt-nucleoids from Pichiajadinii and four other species of yeast. The results suggestthe considerable diversity of the proteins in the mt-nucleoidsof yeasts. (Received March 28, 1996; Accepted June 19, 1996)     

Isolation of giant mitochondrial nucleoids from the yeastSaccharomyces cerevisiae

Summary The yeast cellsSaccharomyces cerevisiae grown up to stationary phase under either anaerobic conditions, or aerobic conditions in the presence of a respiratory inhibitor, antimycin A, had distinctive giant mitochondrial nucleoids (mt-nucleoids) (apparent diameter 0.6–0.9 m) in contrast with the small mt-nucleoids (apparent diameter 0.2–0.4 m) in respiratory-sufficient cells grown aerobically, as revealed by DAPI-fluorescence microscopy. The cytoplasmic respiratory-deficient cells (rho^– cells), which were induced by treatment of wild-type cells with ethidium bromide, showed both giant and small mt-nucleoids of irregular size. In order to examine the structural and functional differences between giant and small mt-nucleoids, the former were successfully isolated from spheroplasts of three different cells by differential centrifugation and centrifugation on a discontinuous sucrose gradient. The isolated giant mt-nucleoids were intact in the morphology and were free of significant contamination by nuclear chromatin. The number of protein components involved in each of three different giant mt-nucleoids was similar to the number in small mt-nucleoids from aerobically grown cells, though a few noticeable differences were also recognized. DNA-binding proteins with molecular masses of 67 kDa, 52 kDa, 50 kDa, 38 kDa, 26 kDa, and 20 kDa were the main components of small mt-nucleoids from aerobically grown cells as detected by chromatography on native DNA-cellulose. In contrast, the 67 kDa and 52 kDa proteins were hardly detected in corresponding fractions of giant mt-nucleoids from anaerobically grown cells and from rho^– cells grown aerobically. On the other hand, mt-nucleoids from aerobically grown cells in the presence of antimycin A seemed to lack the 67 kDa protein but to have a small amount of the 52 kDa protein. This is the first demonstration of the variance of protein species involved in yeast mt-nucleoids according to the respiratory activity of mitochondria.     

Isolation of the mitochondrial nucleoids from yeast Kluyveromyces lactis and analyses of the nucleoid proteins

Mitochondrial (mt) nucleoids were isolated from yeast Kluyveromyces lactis with morphological intactness. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) revealed more than 20 proteins that are associated with the mt-nucleoids. However, the protein profile of the mt-nucleoids of K. lactis was significantly different from that of the mt-nucleoid proteins from Saccharomyces cerevisiae. SDS-DNA PAGE, which detected an Abf2p, a major mitochondrial DNA-binding protein, among the mt-nucleoid proteins of S. cerevisiae on a gel, detected only a 17-kDa protein in the K. lactis mt-nucleoid proteins. The 17-kDa protein was purified as homogeneous from the mt-nucleoids by a combination of acid extraction, hydroxyapatite chromatography and DNA-cellulose chromatography. The 17-kDa protein introduced a negative supercoil into circular plasmid DNA in the presence of topoisomerase I, as does S. cerevisiae Abf2p, and it packed K. lactis mtDNA into nucleoid-like particles in vitro. These results, together with the determination of the N-terminal amino acid sequence, suggested that the 17-kDa protein is an Abf2p homologue of K. lactis and plays structural roles in compacting mtDNA in cooperation with other nucleoid proteins.     

Studies on Plastid-Nuclei (Nucleoids) in Nicotiana tabacum L. II. Disassembly and Reassembly of Proplastid-Nuclei Isolated from Cultured Cells

The effects of various concentrations of NaCl on the compactstructure of proplastid-nuclei (pp-nuclei) isolated from culturedtobacco cells were examined by fluorescence microscopy usinga DNA-specific fluorochrome, 4, 6-diamidino-2-phenylindole.Simultaneously, behavior of the four proplastid DNA-bindingproteins (mol wt: 69kDa, 31 kDa, 30kDa and 14kDa) identifiedpreviously (Nemoto et al. 1988) was investigated by SDS-polyacrylamidegel electrophoresis. When the concentration of NaCl was increased, the isolated pp-nucleiwere gradually dispersed, and at concentrations greater than0.4 M NaCl they were almost completely dispersed. During thisdisassembly process, the 31-kDa and 30-kDa proteins dissociatedfrom the pelletable pp-nuclear fraction to the supernatant at0.1 M NaCl, whereas the 69-kDa and 14-kDa proteins dissociatedto the supernatant only at 0.4 M NaCl. When the concentrationof NaCl was decreased again by dialysis, the pp-nuclei whichhad been dispersed by 2 M NaCl were gradually reassembled intocompact structures which were almost identical to the originalpp-nuclei. During this reassembly process, the 69-kDa and 14-kDaproteins first returned to the pellet fraction, and subsequentlythe 31-kDa and 30-kDa proteins moved into the pellet. This behavior of the proplastid DNA-binding proteins stronglysuggests that the association of these proteins with plastid-DNAis responsible for the compact organization of pp-nuclei. Inaddition, it was indicated that the 69-kDa and 14-kDa proteinsare more tightly bound to plastid-DNA than are the 31-kDa and30-kDa proteins. ⁴Present address: Biological Laboratory, Faculty of Science,Nara Women's University, Nara, 630 Japan. (Received August 24, 1988; Accepted February 28, 1989)     

Studies on Plastid-Nuclei (Nucleoids) in Nicotiana tabacum L. I. Isolation of Proplastid-Nuclei from Cultured Cells and Identification of Proplastid-Nuclear Proteins

We have developed a method of isolating morphologically intactproplastid-nuclei (nucleoids) in large quantities from Nicotianatabacum cultured cells (line BY-2) without contamination bymitochondria and cell-nuclei. Fluorescence microscopy using 4',6-diamidino-2-phenylindole(DAPI) revealed that the compact structure of the isolated proplastid-nuclei(pp-nuclei) was disorganized by DNase I, micrococcal nuclease,proteinase K, 2 M NaCl and 2 M KC1, but was not affected byRNase A, suggesting that the pp-nuclei are compactly organizedby an electrostatic interaction between the proplastid- DNA(pp-DNA) and some protein(s). Although SDS-polyacrylamide gelelectrophoresis showed that the isolated pp-nuclear fractionstill contained a number of polypeptides, only four of them(mol wt: 69 kDa, 31 kDa, 30 kDa and 14 kDa) were found to besolubilized by treatments of the pelletable pp-nuclear fractionwith DNase I, micrococcal nuclease and 2 M NaCl. Furthermore,when the supernatant of the pp-nuclei treated with DNase I wasapplied onto a denatured or a native DNA-cellulose affinitycolumn, these four polypeptides were bound to both DNAs andeluted by raising the NaCl concentration. These findings, taken together, show that these proteins areproplastid DNA-binding proteins and strongly suggest that thepp-nuclei are compactly organized by interaction between thepp-DNA and these proteins. ⁴Present address: Department of Biology, Faculty of Science,University of Tokyo, Hongo, Tokyo 113, Japan. ⁵Present address: School of Food and Nutritional Sciences, Universityof Shizuoka, Yata, Shizuoka 422, Japan. (Received August 13, 1987; Accepted November 9, 1987)     

Immunological characterization of rapeseed myrosinase

A purified 75-kDa myrosinase and a crude rapeseed myrosinase fraction were used as antigens to produce mouse anti-myrosinase monoclonal antibodies. The 75-kDa myrosinase was also used to produce a polyclonal rabbit antiserum. The antiserum and one monoclonal antibody reacted with three distinct rapeseed polypeptides of 75, 70 and 65 kDa (M75, M70 and M65, respectively). A second set of monoclonal antibodies reacted exclusively with the 75-kDa form of myrosinase, and a third set showed specificity towards two components of 52 and 50 kDa (myrosinase-binding proteins, MBP52 and MBP50, respectively). MBP52 and MBP50 lack inherent myrosinase activity, but are nevertheless capable of mediating immunoprecipitation of myrosinase due to their interaction with myrosinase. Gel chromatography and glycerol gradient centrifugation experiments resolved two myrosinase-containing fractions. One of these had an approximate molecular mass of 140 kDa and consisted of disulfide-linked dimers of the 75-kDa myrosinase. The other fraction was heterogeneous in size with molecular masses ranging from 250 kDa to approximately 1 MDa. The high-molecular-mass fractions contained complexes consisting of disulfide-linked 70-kDa and 65-kDa myrosinases and non-covalently bound 52-kDa and 50-kDa myrosinase-binding proteins.     

Microsequence analysis of DNA-binding proteins 7a, 7b, and 7e from the archaebacterium Sulfolobus acidocaldarius

DNA-binding proteins in eubacteria, such as Escherichia coli NS1 and NS2, are generally small basic molecules. In contrast, the archaebacterium Sulfolobus acidocaldarius contains three groups of DNA-binding proteins which have molecular masses of 7, 8, and 10 kDa. In the first group, five proteins (7a-7e) have been identified, while in the second and third group only two proteins each are present, denoted 8a and 8b and 10a and 10b, respectively. In this paper, we present the primary structures of proteins 7a, 7b, and 7e from the first group. All three proteins contain lysyl residues which are monomethylated to different extents. The modified lysines are found in the NH2-terminal regions of all 7-kDa proteins and in the COOH-terminal part of protein 7e. The sequences of the 7-kDa group are highly similar to each other. All of these macromolecules have been shown to interact specifically with DNA. Protein 7e of the 7-kDa group shows the tightest binding to DNA.     

Macromolecules Involved in the Amoeba-Bacteria Symbiosis1

ABSTRACT. In the Amoeba-bacteria symbiosis, rod-shaped Gram-negative bacterial endosymbionts reside within symbiosomes in the host cytoplasm, and the host and symbionts are mutually dependent for survival. Three proteins and one group of lipopolysaccharides (LPS) synthesized by the bacterial endosymbionts and two proteins derived from the host cells have been found to be involved in the host-symbiont interactions, although their respective roles are not yet fully known. The symbiont-derived molecules included proteins with molecular weights of 29 kDa, 67 kDa and 96 kDa and LPS. The 29-kDa protein was most abundant in the host cytoplasm, while the 96-kDa protein and LPS were found mostly on the symbiosome membranes. The 67-kDa protein was a GroEL analog and stayed within the symbionts. The host-derived 43-kDa protein, actin, was selectively accumulated by the symbionts, while the 220/225-kDa protein, spectrin, was attached to the symbiosome membranes. The symbiont genes coding for the 29-kDa and 67-kDa proteins were cloned and sequenced. The 29-kDa protein gene was unique with no relation to any known DNA sequences but has a leucine zipper-like motif, suggesting a possible DNA-binding function. The DNA sequence of the 67-kDa protein gene showed a 70% identity with heat-shock-protein genes of Escherichia coli and Coxiella burnetii.     

A Prolyl Endoproteinase that Acts Specifically on the Extrinsic 18-kDa Protein of Photosystem II: Purification and Further Characterization

An endoproteinase, which specifically cleaves the Pro12-Leu13bond of the extrinsic 18-kDa protein of PSII, was purified fromPSII membranes of spinach. The presence of 0.05% (w/v) Tween20 and 1 M NaCl was essential for maintenance of proteolyticactivity during the purification. The molecular mass of theenzyme was estimated to be 95 kDa by gel-filtration chromatography.Active fractions contained a polypeptide of 165 kDa that wasconverted into diffusely stained polypeptides of 54 kDa uponreduction with dithiothreitol. The K_m of the 18-kDa proteinin the proteolytic reaction was 0.3 µM. Inhibition ofthe proteolysis by compounds that contain prolyl bonds revealedthat both a prolyl bond and a positive charge are necessaryfor interaction with the proteinase, but some other structuralfactor(s) must also be involved in the high-affinity interactionbetween the proteinase and the 18-kDa protein. Reconstitutionof NaCl-treated PSII membranes with the 23-kDa protein and/orthe 18-kDa protein revealed that the 18-kDa protein was notcleaved by the proteinase when the substrate protein was functionallyassociated with the membranes. A comparison of the propertiesof the proteinase with those of a proline-specific endopeptidasefrom Flavobacterium suggests that these enzymes are quite differentin terms of substrate specificity. (Received December 13, 1993; Accepted March 24, 1994)     

DNA-binding proteins of mammalian mitochondria

Acid-soluble proteins were isolated from liver and spleen mitochondria and their ability to form complexes with DNA was investigated. According to electrophoresis data, acid-soluble proteins include about 20 polypeptides ranging in the molecular mass from 10 to 120 kDa. It was found that acid-soluble proteins form stable DNA-protein complexes at a physiological NaCl concentration. Different polypeptides possess different degrees of DNA affinity. There is no significant difference between DNA-binding proteins of mitochondria from liver and those from spleen as to their ability to form complexes with mtDNA and nDNA. In the presence of 5 microg of DNA most polypeptides were bound to DNA, and further increase in DNA amount affected little the binding of proteins to DNA. There was no distinct difference in DNA-protein complex formation of liver mitochondrial acid-soluble proteins with nDNA or mtDNA. Also, it was detected that with these mitochondrial acid-soluble proteins, proteases that specifically cleave these proteins are associated. It was shown for the first time that these proteases are activated by DNA. DNA-binding proteins including DNA-activated mitochondrial proteases are likely to participate in the regulation of the structural organization and functional activity of mitochondrial DNA.     

Location of a synergistic factor in the capsule of a granulosis virus of the armyworm, Pseudaletia unipuncta

A synergistic factor (SyF), which enhanced the infection of nuclear polyhedrosis viruses, was purified from capsules of a Pseudaletia unipuncta granulosis virus (Hawaiian strain) by immune affinity chromatography. The isolated SyF consisted primarily of a protein with molecular mass 98 kDa. The recovery rate depended on the alkali used to dissolve the capsules: the highest rate occurred with 0.05 M Na2CO3-0.05 M NaCl, followed in turn with 0.02-0.05 M NaOH and 0.04 M NaOH-0.05 M glycine. The solubilized components from untreated capsules contained 98- and 100-kDa proteins in addition to the matrix protein (29 kDa) and its decomposed products, while those from heat-treated capsules contained only the 100-kDa protein. Virons liberated from the capsules with the glycine buffer contained three proteins (33, 98, and 100 kDa) serologically related to the SyF. Immunoelectron microscopy of infected tissue and purified virions revealed the localization of the SyF antigens on the viral envelope.     

Genetic Variability in Recovery Growth and Synthesis of Stress Proteins in Response to Polyethylene Glycol and Salt Stress in Finger Millet

Marked differences were found among 28 finger millet genotypes(Eleusine coracana Gaertn.) in acquired tolerance to osmoticstress as assessed by the recovery of root growth from severestress [-1·2 MPa polyethylene glycol, (PEG) or 400 mMNaCl]. However, these differences in tolerance were observedonly when the seedlings were subjected to a preceding mild inductionstress (-0·6 MPa PEG or 200 mM NaCl). In two contrastinggenotypes, synthesis of stress-induced proteins was studied.Proteins with apparent molecular weight of 70-72, 52, 37, 34and 23 kDa were synthesized in the highly responsive genotype(GE 415) and poorly responsive (VL 481) genotype following amild induction stress (200 mM NaCl). However, GE-415 synthesizeda 54 kDa protein that was not observed in VL-481. Addition ofabscisic acid (ABA) to the induction medium containing 200 mMNaCl enhanced the acquired tolerance of finger millet seedlingsover those without ABA in association with the appearance ofseveral ABA-responsive proteins. GE-415 required much less ABAthan VL-481 to obtain the same response. With 10 µM ABA+ 200 mM, A NaCl induction stress, GE-415 had significantlyhigher endogenous ABA. In association with higher levels ofABA, GE-415 had greater recovery root growth following severestress from 600 mM NaCl. Pretreatment with 10 µM ABA +200 mM NaCl induced several proteins with apparent molecularweights of 70-72, 54, 45, 36, 29 and 21 kDa in both genotypes.Qualitatively, GE-415 synthesized a unique 23-24 kDa proteinand quantitatively there was significantly more of the 21 kDaprotein in GE-415 compared to VL-481. The results indicate thatthe synthesis of stress proteins is correlated with the observedvariation in acquired tolerance of the two genotypes.Copyright1995, 1999 Academic Press Eleusine coracana Gaertn., salinity, polyethylene glycol, stress proteins, ABA, ABA-responsive proteins, finger millet seedlings     

Properties of Two N-Linked Glycoproteins Associated with the Nuclear Envelope in Mung Bean Hypocotyls

Nuclei from mung bean (Vigna radiata) hypocotyls contained twoglycoproteins of 50 and 49 kDa, respectively, that reacted withconcanavalin A. The glycoproteins were released from the nuclearenvelope by treatment with 2 M KCl but not with nucleases. Theglycoproteins, tentatively named gp50 and gp49, were isolatedand characterized. Gel-permeation chromatography suggested thatgp50 and gp49 seem to exist as a complex with other components.The glycoproteins could be detected only in the nuclear fractionby immunoblot analysis with specific antibodies, and they werenot detected in endoplasmic reticulum, plasma membrane, vacuolarmembrane or mitochondria. Agglutinin I from Ulex europeaus,peanut agglutinin, soybean agglutinin and wheat germ agglutininall failed to bind to the glycoproteins. Treatment with glycopeptidaseF removed all oligosaccharides from the glycoproteins and decreasedtheir molecular masses by about one thousand daltons each. Theseresults suggest that the glycoproteins contained N-linked, high-mannose-typeoligosaccharides with six or seven hexose residues. gp50 andgp49 seemed to be isoforms of a single glycoprotein becausethe two proteins had some common properties. Nuclear fractionsfrom azuki bean (Phaseolus angularis) and soybean (Glycine max)contained proteins that were immunologically similar to gp50and gp49. (Received March 18, 1995; Accepted May 24, 1995)     

Composition and DNA-binding properties of the nuclear matrix proteins from mammalian cell nuclei

A rapidly sedimenting DNA-protein complex was isolated from nuclear lysates in 2 M NaCl and characterized with regard to its polypeptide composition and the DNA-binding properties of the purified proteins. The complex consists of the nuclear matrix with attached DNA. Electrophoresis in SDS-polyacrylamide gels revealed two major and five minor polypeptide bands, mainly in the 60 to 75 kDa molecular weight region. The DNA-matrix complex dissociated into free DNA and proteins in the presence of 2 M NaCl and 5 M urea. The proteins could be purified by chromatography on hydroxyapatite and showed a strong tendency to reassociate at 0.15 M NaCl concentration in the absence of urea. DNA was bound to the reassociated proteins at 0.15 M NaCl concentration. Part of the DNA-protein complex was stable at 1 M NaCl concentration. The binding appeared to be random with regard to the DNA sequence.     

Isolation of the D1 Protein and a 28-kDa Fragment of the D2 Protein from Spinach Photosystem II Membranes

The 32-kDa D1 protein, which contained no lysine in spinachchloroplasts, as deduced from its DNA code, was isolated byhigh-performance gel permeation chromatography in the presenceof 0.1% SDS and 4 M urea. Three proteins of the photosystemII reaction center complex have a molecular mass of 30–35kDa, and two, the D2 protein and the peripheral 33-kDa protein,were severed into peptide fragments by Achromobacter lysyl endopeptidase(EC 3.4.14.50 [EC] ) before the chromatography. The isolated D1 proteindid not contain chlorophylls and pheophytins but had an absorptionmaximum at 265 nm probably due to bound plastoquinone. A peptidefragment of 28 kDa from the D2 protein was also isolated fromspinach photosystem II membranes and the wheat photosystem IIreaction center. Antibodies raised against the 28-kDa peptidefrom wheat bound to the 34-kDa D2 protein, which suggested thatthis peptide was the largest sequence of Aspl4-Lys265. The fragmentof wheat D2 protein showed absorption maxima at 413 and 682nm attributable to bound pheophytin that probably had been convertedfrom chlorophyll a during the isolation process. (Received June 29, 1987; Accepted October 21, 1987)