Accumulation of Uridinediphospho-N-acetylmuramyl-peptides Induced by Glycine and Penicillin

The genes POX2 and POX4, which encode the subunits (PXP-2 and PXP-4) of peroxisomal fatty acyl-coenzyme A oxidase of Candida tropicalis, were introduced into the related yeast Candida maltosa. The cells transformed with POX2 or POX4 gave much PXP-2 or PXP-4 in the purified peroxisomes. The polypeptides associated with the heterologous organelle were resistant to added protease, implying that they were transported into the peroxisomes. Genes for curtailed versions of PXP-4 were constructed in vitro and introduced into the host cells. Peptide-C, the COOH-terminal two-thirds of PXP-4, was efficiently transported into the host peroxisomes, and the polypeptide containing the NH₂-terminal one-third was also, in much lesser amount. These and other results suggested that there were at least two regions of peroxisomal targeting information in PXP-4 and the primary information was internal. The deletions in Peptide-C inhibited the transport of many, but not all, of the host-cell peroxisomal polypeptides. This suggested heterogeneous transport systems on the peroxisomal membrane.     

A novel peroxisomal nonspecific lipid-transfer protein from Candida tropicalis. Gene structure, purification and possible role in beta-oxidation

We have sequenced the nucleotides of the gene POX18 that encodes PXP-18, a major peroxisomal polypeptide inducible by oleic acid in the yeast Candida tropicalis. POX18 had a single open reading frame of 127 amino acids. Some 33% of the amino acid sequence of the predicted basic polypeptide (13,805 Da), was identical to that of the nonspecific lipid-transfer protein (sterol carrier protein 2) from rat liver. PXP-18, purified to near homogeneity from isolated peroxisomes, had an amino-terminal sequence identical to that of the predicted polypeptide except for the initiator methionine, and had nonspecific lipid-transfer activity comparable to that of its mammalian equivalents. Unexpectedly, PXP-18 lacked the cysteine residue thought to be essential for the activity of this protein in mammals. RNA blot analysis showed that the POX18 gene was expressed exclusively in cells grown on oleic acid, suggesting that PXP-18 has a role in the beta-oxidation of long-chain fatty acids. PXP-18 modulated acyl-coenzyme A oxidase activity at low pH.     

Peroxisomal acyl-coenzyme A oxidase multigene family of the yeast Candida tropicalis; nucleotide sequence of a third gene and its protein product

We have determined the complete nucleotide sequence of gene POX2, which encodes one of the major peroxisomal polypeptides (PXPs) of Candida tropicalis. POX2 is linked to gene POX4, which codes for a subunit (PXP-4) of long-chain acyl-CoA oxidase. Southern blot analysis revealed that POX2 had a significant homology to POX4, and also to gene POX5 which encodes a subunit (PXP-5) of the isozyme of acyl-CoA oxidase. PXP-2, the protein product of POX2, was co-purified with PXP-4 from the isolated peroxisomes. PXP-2 itself was a flavoprotein and likely to form an equimolar complex with PXP-4, although its enzymatic activity was uncertain. POX2 corresponds to a single open reading frame of 724 amino acids and has no introns. The N-terminal sequence and the calculated Mr of the deduced polypeptide were consistent with those of isolated PXP-2. The primary structure was highly homologous to those of PXP-4 and PXP-5 in respect of the amino acid sequence and the hydropathy profile. We conclude that POX2 is a third gene of the peroxisomal acyl-COA oxidase multigene family.     

Reversible alteration of hepatic messenger RNA species for peroxisomal and non-peroxisomal proteins induced by the hypolipidaemic drug Wy-14,643.

Extensive peroxisomal proliferation in the hepatic parenchymal cells was observed when male rats were given a diet containing 0.1% Wy-14,643 [( 4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio]acetic acid), a potent lipid-decreasing drug. This drug also caused a marked increase in the concentrations of the mRNA species coding for four proteins with Mr 77000, 61000, 43000 and 31000, and a similar decrease in the concentrations of three mRNA species coding for proteins of Mr 25000, 24000 and 19000. Specific immunoprecipitation studies identified the proteins of Mr 19000, 43000 and 77000 as alpha 2u-globulin, 3-ketoacyl-CoA thiolase (EC 2.3.1.16) and enoyl-CoA hydratase (EC 4.2.1.17) respectively. Comparisons of the Mr values suggest that the 61000- and 31000-Mr proteins may be equivalent to two additional peroxisomal enzymes, namely catalase (Mr 61000) and uricase (Mr 31000). The identity of the mRNA species coding for the 25000- and 24000-Mr proteins is at present unknown.     

Sequence analysis and expression of the two genes for elongation factor 1 alpha from the dimorphic yeast Candida albicans.

Two Candida albicans genes that encode the protein synthesis factor elongation factor 1 alpha (EF-1 alpha) were cloned by using a heterologous TEF1 probe from Mucor racemosus to screen libraries of C. albicans genomic DNA. Sequence analysis of the two clones showed that regions of DNA flanking the coding regions of the two genes were not homologous, verifying the presence of two genes, called TEF1 and TEF2, for EF-1 alpha in C. albicans. The coding regions of TEF1 and TEF2 differed by only five nucleotides and encoded identical EF-1 alpha proteins of 458 amino acids. Both genes were transcribed into mRNA in vivo, as shown by hybridization of oligonucleotide probes, which bound specifically to the 3' nontranslated regions of TEF1 and TEF2, respectively, to C. albicans total RNA in Northern (RNA) blot analysis. The predicted EF-1 alpha protein of C. albicans was more similar to Saccharomyces cerevisiae EF-1 alpha than to M. racemosus EF-1 alpha. Furthermore, codon bias and the promoter and termination signals of the C. albicans EF-1 alpha proteins were remarkably similar to those of S. cerevisiae EF-1 alpha. Taken together, these results suggest that C. albicans is more closely related to the ascomycete S. cerevisiae than to the zygomycete M. racemosus.     

Yarrowia lipolytica Cells Mutant for the Peroxisomal Peroxin Pex19p Contain Structures Resembling Wild-Type Peroxisomes

PEX genes encode peroxins, which are proteins required for peroxisome assembly. The PEX19 gene of the yeast Yarrowia lipolytica was isolated by functional complementation of the oleic acid-nonutilizing strain pex19-1 and encodes Pex19p, a protein of 324 amino acids (34,822 Da). Subcellular fractionation and immunofluorescence microscopy showed Pex19p to be localized primarily to peroxisomes. Pex19p is detected in cells grown in glucose-containing medium, and its levels are not increased by incubation of cells in oleic acid-containing medium, the metabolism of which requires intact peroxisomes. pex19 cells preferentially mislocalize peroxisomal matrix proteins and the peripheral intraperoxisomal membrane peroxin Pex16p to the cytosol, although small amounts of these proteins could be reproducibly localized to a subcellular fraction enriched for peroxisomes. In contrast, the peroxisomal integral membrane protein Pex2p exhibits greatly reduced levels in pex19 cells compared with its levels in wild-type cells. Importantly, pex19 cells were shown by electron microscopy to contain structures that resemble wild-type peroxisomes in regards to size, shape, number, and electron density. Subcellular fractionation and isopycnic density gradient centrifugation confirmed the presence of vesicular structures in pex19 mutant strains that were similar in density to wild-type peroxisomes and that contained profiles of peroxisomal matrix and membrane proteins that are similar to, yet distinct from, those of wild-type peroxisomes. Because peroxisomal structures form in pex19 cells, Pex19p apparently does not function as a peroxisomal membrane protein receptor in Y. lipolytica. Our results are consistent with a role for Y. lipolytica Pex19p in stabilizing the peroxisomal membrane.     

New aspects of sterol carrier protein 2 (Nonspecific lipid-transfer protein) in fusion proteins and in peroxisomes

Sterol carrier protein 2 (SCP2) is a 13-kDa peroxisomal protein, identical to nonspecific lipidtransfer protein, and stimulates various steps of cholesterol metabolism in vitro. Although the name is reminiscent of acyl carrier protein, which is involved in fatty acid synthesis, SCP2 does not bind to lipids specifically or stoichiometrically. This protein is expressed either as a small precursor or as a large fusion (termed SCPx) that carries at its C-terminal the complete sequence of SCP2. SCPx exhibits 3-oxoacyl-CoA thiolase activity, as well as sterol-carrier and lipid-transfer activities. The N- and C-terminal parts of SCPx are similar to the nematode protein P-44 and the yeast protein PXP-18, respectively. P-44, which has no SCP2 sequence, thiolytically cleaved the side chain of bile acid intermediate at a rate comparable to that of SCPx. This, together with the properties of other fusions with SCP2-like sequence, suggests that the SCP2 part of SCPx does not play a direct role in thiolase reaction. PXP-18, located predominantly inside peroxisomes, is similar to SCP2 in primary structure and lipid-transfer activity, and protects peroxisomal acyl-CoA oxidase from thermal denaturation. PXP-18 dimerized at a high temperature, formed an equimolar complex with the oxidase subunit, and released the active enzyme from the complex when the temperature went down. This article attempts to gain insight into the role of SPC2, and to present a model in which PXP-18, a member of the SCP2 family, functions as a molecular chaperone in peroxisomes.     

Analysis of sequences from the extremely A + T-rich genome of Plasmodium falciparum

The genome of the human malaria parasite Plasmodium falciparum has an A + T content of about 82%, higher than any other organism whose DNA has been characterized. Computer analysis of 36 kb of available nucleotide sequences from this species showed that the coding regions, with an A + T content of 69.0%, are flanked by more A + T-rich regions of 86.0% A + T. Within the coding sequences, the A/T ratio was 1.68 in the mRNA sense strand, and overall A + T content in the three codon positions increased in the order 1st-2nd-3rd position. Codons with T or especially A in the third position were strongly preferred. Codon usage among individual parasite genes was very similar compared to genes from other species. Dinucleotide frequencies for the parasite DNA were close to those expected for a random sequence with the known base composition, except that the CpG frequency in the coding sequences was low.     

Two genes encode the major membrane-associated protein of methanol-induced peroxisomes from Candida boidinii

A massive proliferation of peroxisomes occurs in the yeast Candida boidinii when methanol is utilized as the sole carbon source; these peroxisomes contain the enzymes which catalyze the initial steps of methanol utilization. The most abundant peroxisomal membrane-associated protein has an apparent molecular mass of 20 kDa and is termed PMP20. We report the isolation of two genes that encode very similar forms of PMP20; this is the first report of genes that encode proteins associated with peroxisomal membranes. Southern analysis demonstrates that the two genes are on different loci, although there are several homologous regions of both 5'- and 3'-untranslated sequence. One of the areas of 5' homology is within the untranslated region of the mRNA. Within the coding region there are 35 base differences between the two genes that are reflected in only five amino acid differences. The mRNAs representing both genes of PMP20 are induced in cells grown in methanol-containing medium and are below detection in cells grown in glucose. S1 nuclease protection analysis indicates that there is a 2.5-fold difference in mRNA expression between the two genes when induced. The predicted sequences of both PMP20 genes show the absence of a cleaved amino-terminal leader sequence and the presence of only 1 cysteine residue. In agreement with previous biochemical data suggesting a peripheral association of this protein with the membrane (Goodman, J. M., Maher, J., Silver, P. A., Pacifico, A., and Sanders, D. (1986) J. Biol. Chem. 261, 3464-3468), there are no obvious membrane spanning regions predicted in the sequences. Both PMP20 gene products contain the carboxyl-terminal sequence AKL, similar to the putative SKL peroxisomal sorting sequence (Gould, S. J., Keller, G.-A., and Subramani, S. (1988) J. Cell Biol. 107, 897-905).     

Identification of multiple cytochrome P450 genes belonging to the CYP4 family in Xenopus laevis: cDNA cloning of CYP4F42 and CYP4V4

In order to obtain cDNA clones coding for CYP4 proteins in frog Xenopus laevis, degenerate primers were designed utilizing the conserved sequences of known CYP4s and were used to amplify partial cDNA fragments from liver mRNA. Five new CYP genes were identified. Three of these genes, XL-1, -2 and -3, were assigned to the CYP4T subfamily found previously in fish and amphibians. The other two genes, XL-4 and XL-5, were quite similar to CYP4F and CYP4V subfamilies, respectively. Subsequently, two full-length cDNA clones corresponding to XL-4 and XL-5 were isolated and characterized. The resultant cDNAs, designated as CYP4F42 and CYP4V4, had open reading frames encoding proteins of 528 and 520 residues, respectively. RT-PCR analysis indicated that the expression of CYP4F42 was limited to the liver, kidney, intestine and brain. In contrast, CYP4V4 mRNA was expressed ubiquitously.     

Nucleotide sequence of a protamine component CII gene of Salmo gairdnerii.

We have isolated, using nick-translated cloned protamine cDNA's as probes, several genomic clones containing protamine gene sequences from a Charon 4A library of Eco R1 digested rainbow trout (Salmo gairdnerii) DNA. One clone was chosen for detailed study and the 2.5 kbp Bam HI-Eco R1 restriction fragment containing the gene was subcloned in the plasmid pBR322. A 920 bp Bg1 II - Bam HI restriction fragment contains a sequence coding for protamine component CII as well as regions 5' and 3' to the mRNA coding portion. Present in the region 5' to the mRNA coding sequence are the promoter associated signals "TATA" box and "CAAT" box. The 5' untranslated region of the mRNA whose length and sequence were not established from the cDNA clones (1) was determined by nuclease mapping and starts within a sequence similar to the "capping signal" found in other genes. The protamine gene for CII contains no introns, a situation common to most histone genes, but, unlike the histone genes does not occur close to other protamine genes in a "cluster".