Evidence that trimethylation of iso-I-cytochrome c from Saccharomyces cerevisiae affects interaction with the mitochondrion

The role of key residues in structure, function, and stability of cytochrome-c

Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.

Lysine methylation of nonhistone proteins is a way to regulate their stability and function

This review is devoted to the dramatically expanding investigations of lysine methylation on nonhistone proteins and its functional importance. Posttranslational covalent modifications of proteins provide living organisms with ability to rapidly change protein activity and function in response to various stimuli. Enzymatic protein methylation at different lysine residues was evaluated in histones as a part of the "histone code". Histone methyltransferases methylate not only histones, but also many nuclear and cytoplasmic proteins. Recent data show that the regulatory role of lysine methylation on proteins is not restricted to the "histone code". This modification modulates activation, stabilization, and degradation of nonhistone proteins, thus influencing numerous cell processes. In this review we particularly focused on methylation of transcription factors and other nuclear nonhistone proteins. The methylated lysine residues serve as markers attracting nuclear "reader" proteins that possess different chromatin-modifying activities.

Cytochrome c impaled: investigation of the extended lipid anchorage of a soluble protein to mitochondrial membrane models

Cyt c (cytochrome c) has been traditionally envisioned as rapidly diffusing in two dimensions at the surface of the mitochondrial inner membrane when not engaged in redox reactions with physiological partners. However, the discovery of the extended lipid anchorage (insertion of an acyl chain of a bilayer phospholipid into the protein interior) suggests that this may not be exclusively the case. The physical and structural factors underlying the conformational changes that occur upon interaction of ferrous cyt c with phospholipid membrane models have been investigated by monitoring the extent of the spin state change that result from this interaction. Once transiently linked by electrostatic forces between basic side chains and phosphate groups, the acyl chain entry may occur between two parallel hydrophobic polypeptide stretches that are surrounded by positively charged residues. Alteration of these charges, as in the case of non-trimethylated (TML72K) yeast cyt c and Arg91Nle horse cyt c (where Nle is norleucine), led to a decline in the binding affinity for the phospholipid liposomes. The electrostatic association was sensitive to ionic strength, polyanions and pH, whereas the hydrophobic interactions were enhanced by conformational changes that contributed to the loosening of the tertiary structure of cyt c. In addition to proposing a mechanistic model for the extended lipid anchorage of cyt c, we consider what, if any, might be the physiological relevance of the phenomenon.

Cytochrome c methyltransferase, Ctm1p, of yeast

Cytochromes c from plants and fungi, but not higher animals, contain methylated lysine residues at specific positions, including for example, the trimethylated lysine at position 72 in iso-1-cytochrome c of the yeast Saccharomyces cerevisiae. Testing of 6,144 strains of S. cerevisiae, each overproducing a different open reading frame fused to glutathione S-transferase, previously revealed that YHR109w was associated with an activity that methylated horse cytochrome c. We show here that this open reading frame, denoted Ctm1p, is specifically responsible for trimethylating lysine 72 of iso-1-cytochrome c. Unmethylated forms of cytochrome c but not other proteins or nucleic acids are methylated in vitro by Ctm1p produced in S. cerevisiae or Escherichia coli. Iso-1-cytochrome c purified from a ctm1-Delta strain is not trimethylated in vivo, whereas the K72R mutant form, or the trimethylated Lys-72 form of iso-1-cytochrome c, are not significantly methylated by Ctm1p in vitro. Like apocytochrome c, but in contrast to holocytochrome c, Ctm lp is located in the cytosol, consistent with the view that the natural substrate is apocytochrome c. The ctm1-Delta strain lacking the methyltransferase did not exhibit any growth defect on a variety of media and growth conditions, and the unmethylated iso-1-cytochrome c was produced at the normal level and exhibited the normal activity in vivo. Ctm1p and cytochrome c were coordinately regulated during anaerobic to aerobic transition, a finding consistent with the view that this methyltransferase evolved to act on cytochrome c.

Sequence requirement for trimethylation of yeast cytochrome c

Lysine 72 (using the vertebrate numbering system) is trimethylated in cytochromes c from fungi and plants but not from higher animals. We have investigated the characteristics of an amino acid sequence required for trimethylation of lysine 72 by examining 21 altered iso-1-cytochromes c from Saccharomyces cerevisiae having single replacements in the region encompassing residues 67 through 77. These results indicated that tyrosine 74 is critical for trimethylation of lysine 72, whereas replacements at other positions did not produce significant diminutions. Various replacements of tyrosine 74 resulted in different levels of inhibition, with the Y74F replacement causing no significant reduction, and the Y74E and Y74K replacements completely or almost completely preventing trimethylation of lysine 72. However, other similarly spaced lysine and tyrosine residues at other sites in the protein did not result in trimethylation of the lysine residue. Thus, a properly situated aromatic residue, determined by the overall conformation of apocytochrome c in the vicinity of lysine 72, appears to be essential for trimethylation.

The relationship between the trimethylation of lysine 77 and cytochrome c metabolism in Saccharomyces cerevisiae

1. Site directed mutations were constructed in the yeast iso-1-cytochrome c gene adjacent to the lysine 77 (methylation site) codon. 2. These mutant genes were then cloned and transformed into the S. cerevisiae strain B-6642 which contains a deficiency in the iso-1-cytochrome c gene. 3. The resulting transformants were screened for cytochrome c production using gel electrophoresis. 4. Amino acid analysis of the mutated cytochromes c demonstrated varying levels of trimethyllysine formation, depending on the nature of the site directed mutation. 5. The resulting transformants were then used as tools in order to investigate the relationship between trimethyllysine formation and various aspects of cytochrome c metabolism including protein stability and heme conjugation.

Expression of recombinant cytochromes c from various species in Saccharomyces cerevisiae: post-translational modifications

A complete protocol for the expression of recombinant cytochrome c genes from yeast, Drosophila melanogaster, and rat in a yeast strain, GM-3C-2, which does not express its own cytochromes c is described. The construction of the expression vectors, transformation and large-scale growth of the yeast, and preparation and purification of the recombinant cytochromes c are described. It was found that, contrary to the way yeast modifies its own cytochromes c, the recombinant proteins were partially acetylated at their N-terminus, except for the drosophila protein, which remained entirely unblocked. Furthermore, the yeast and rat proteins were close to fully trimethylated at lysine 72, while the drosophila protein could be separated chromatographically into forms containing tri-, di-, mono-, and unmethylated lysine 72 showing corresponding resonances in the NMR spectrum. These observations emphasize that, in employing expression procedures to obtain native or mutant forms of cytochrome c, it is essential to identify the variety and extent of post-translational modifications and to separate the preparation into pure monomolecular species. Otherwise, it may become impossible to distinguish between the influence of a site-directed mutation and unexamined post-translational modifications.

Further investigations regarding the role of trimethyllysine for cytochrome c uptake into mitochondria

1. A mutant of the iso-1-cytochrome c gene from Saccharomyces cerevisiae has been constructed which contains an Arg codon, replacing the normal trimethylated Lys at position 77. 2. This mutated gene was cloned into a pGem 1 vector and used for the in vitro translation of yeast iso-1-cytochrome c. 3. Utilizing an in vitro mitochondria binding assay, it was found that the mutant cytochrome c could transverse the yeast mitochondrial membrane, however the amount of protein incorporated was 3-fold less that of the trimethylated wild type. 4. Omission of the protein methyltransferase from assays containing the wild type cytochrome c caused only a slight reduction (15%) in the amount of protein incorporated. 5. These results suggest while the lysine residue 77 of apocytochrome c is important for mitochondria uptake, the methylation of this residue seems to play a relatively minor role.

Effect of enzymatic methylation of yeast iso-1-cytochrome c on its isoelectric point

Yeast iso-1- unmethylated and methylated apocytochrome c were synthesized in vitro by translating yeast cytochrome c mRNA, and by subsequently methylating the protein product. Unmethylated and methylated iso-1-holocytochrome c were extracted from Saccharomyces cerevisiae. By employing a column isoelectrofocusing technique, the pI values of these proteins were determined. The pI values of unmethylated and methylated apocytochrome c were found to be 9.60 and 8.70, respectively, with a difference of 0.90 pI unit. On the other hand, the pI values of unmethylated and methylated holocytochrome c were 9.72 and 9.68, respectively, with a difference of 0.04 unit. Therefore, although the pI values of both apo- and holocytochrome c decreased by methylation, methylation of apocytochrome c had a more profound effect on the pI of the protein. The result also indicated that conjugation of heme to apocytochrome c increased its pI value, resulting in the more "compact" and basic structure of the protein. The observed magnitude of the pI change subsequent to the methylation of apocytochrome c (decrease of 0.90 unit) seemed to be contradictory to the predicted increase in the value, since the positive charge is fixed on the quaternary amino group of trimethyllysine and there is no proton to titrate. Trimethylation of epsilon-NH2 group of Res-72 lysine of apocytochrome c could disrupt any possible hydrogen bond formed by the nitrogen atom of Res-72 lysine residues, as visualized by a space-filling model. The model and observed shift in the "effective charge" of the protein strongly suggest that conformational change in the apoprotein takes place upon methylation. This presumably altered conformation along with the decrease in pI caused by methylation may play a role in enhancement of apocytochrome c import into mitochondria.

Histone binding to isolated rat liver nuclei

Calf thymus histone H3 bound irreversibly to the isolated rat liver nuclei. The rate and extent of binding was a function of the incubation period and the concentration of both H3 and nuclei, but independent of the temperature. The binding was saturable and was inhibited by simultaneous presence of various histones. Approximately 94% of the bound H3 was associated with nuclear membrane fraction.

Enzymatic trimethylation of lysine-72 in cytochrome c

The present observations are the continuation of our earlier study on the physicochemical mechanism of protein-lysine methylation. In this paper the electrophoretic behaviour (pI values) of two chemically modified horse heart cytochromes c at lysine-72 with trifluoromethylphenylcarbamoyl (neutral group) or carboxydinitrophenyl (acidic group) is compared with the enzymatically methylated cytochrome c. The results indicate that although both chemically modified cytochromes c have lower pI values than the unmodified cytochrome c, the enzymatic methylation appears to be much more efficient in lowering the pI values of the protein than the chemical modification. Furthermore, the lowering of the pI value of cytochrome c by enzymatic methylation is highly dependent on the urea concentration. The presence of urea reduces the effect of methylation on the protein molecule and the difference in pI values virtually disappears with the increasing concentration of urea (6 M), which essentially disrupts the protein tertiary structure.

Cytochrome c specific methylase from wheat germ

The cytochromes c of plants (e.g., wheat germ) possess two trimethyllysines, residues 72 and 86. In order to investigate the nature of these methylations, we have purified a cytochrome c specific methylase S-adenosylmethionine: protein(lysine) N-methyltransferase (protein methylase III) from wheat germ 135-fold. The in vitro site of methylation by both the purified enzyme and crude wheat germ extract toward various forms of horse heart cytochrome c was localized by two dimensional peptide mapping, Aminex A-5 column peptide analysis, and CNBr cleavage analysis to be the residue 72 lysine. However, no additional sites, in particular residue 86, were seen to be methylated. Although the enzyme is highly specific toward cytochrome c as an in vitro protein substrate, avian cytochromes c are seen to be much better substrates than those from mammalian sources. The enzyme possesses an extremely low Km for apocytochrome c (1.21 microM), suggesting that methylation may occur before heme attachment in vivo. Various S-adenosyl-L-homocysteine analogues were tested for their inhibitor capability toward the enzyme; it was observed that only the D and L forms of S-adenosylhomocysteine are inhibitors while analogues modified in the adenine or homocysteine moieties do not possess inhibitory capability. Results from the Aminex A-5 column chromatography of horse heart cytochrome c chymotryptic digest showed the N epsilon-methyl-, N epsilon-dimethyl-m and N epsilon-trimethyllysine forms of the residue 68-74 peptide to elute earlier than the unmethylated form. This results suggest that the methylated peptides are less basic than the unmethylated form.

Enzymatic trimethylation of residue-72 lysine in cytochrome c. Effect on the total structure

A highly purified protein methylase III from Neurospora crassa or Saccharomyces cerevisiae specifically methylates a single lysine residue of position 72 of horse heart cytochrome c. The enzymatically methylated cytochrome c has been separated from the unmethylated counterpart species by isoelectric focusing. Simultaneously, the pI values of these two species were found to be 9.49 and 10.03, respectively. Since methyl substitution increases the basicity associated with the epsilon-amino group of lysine residues, the observed decrease in pI value is in opposition to the predicted increase. Space-filling models revealed the possibility of a hydrogen bond between the oxygen of amide of residue-70 asparagine and the epsilon-amino nitrogen of residue-72 lysine in unmethylated horse heart cytochrome C. the enzymatic methylation of residue-72 lysine tends to dissociate this hydrogen bond, thereby possibly inducing the shift of 'effective charge' of the protein molecule. This paper also deals with the pI values of cytochromes c from 13 different sources, determined by the isoelectric focusing technique.

Interaction of cytochrome c with the phosphorprotein phosvitin

Candida krusei cytochrome c forms a molecular complex with phosphorprotein phosvitin in weakly alkaline solution of low ionic strength. At most, about 22 molecules of cytochrome c bind to a phosvitin molecule. The complex at the binding ratio below about 11 (half of the maximum ratio) as a much higher binding strength. Several lines of evidence indicate that the marked difference in the binding strength is due to the difference in negative charges on phosvitin molecule concerned in the binding of a cytochrome c molecule. The phosvitin-bound cytochrome c seems to have a preferred orientation with the front surface of the molecule containing the exposed heme edge in contact with the phosvitin molecule.