characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program genemark

DNA RESEARCH 1, 263-269 (1994) Characteristic Features of the Nucleotide Sequences of Yeast Mitochondrial Ribosomal Protein Genes as Analyzed by Computer Program GeneMark Katsumi ISONO,1'* James D MCININCH, and Mark BORODOVSKY2 Department of Biology, Faculty of Science, Kobe University, Rokkodai, Kobe 657, Japan1 and Georgia Institute of Technology, School of Biology, Atlanta, Georgia 30332, U.S.A.2 (Received 25 December 1994) Introduction The rapid accumulation of nucleotide sequence data of various organisms has raised a challenging theme not only to molecular biologists but also to those who are interested in the analysis of biological information contained in such data Various lines of experimental evidence have suggested how a gene is recognized by transcription factors, RNA polymerases, repressor molecules, as well as co-factors associated with them Also, how a pre-messenger RNA is spliced, modified with capping and poly(A)-adding enzymes, etc has been extensively analyzed and there are many well documented cases of them in several organisms Nonetheless, it is often not so easy to predict just at which nucleotide within a sequence a gene, or a protein-coding sequence, starts Experimentally, presence of a promoter for a given gene can be proven by the combination of several biochemical and molecular biological methods However, prediction of a promoter in a given nucleotide sequence of even such a well studied organism as Escherichia coli by using a computer program alone is not always successful During the course of our systematic sequence analCommunicated by Mituru Takanami * To whom correspondence should be addressed Tel +8178-803-0553, Fax +81-78-803-0489, E-mail: isono scitec.kobe-u.ac.jp ysis of the E coli genome, we found that the computer program GeneMark developed by Borodovsky and McIninch1 was very useful in predicting likely genes in the nucleotide sequence data.2"4 The algorithm of this program is based on the statistical models (nonhomogeneous Markov chain models) for the appearance of short stretches of nucleotide that differ in proteincoding regions and non-coding regions One of the obvious reasons for this is the presence of codons consisting of three nucleotides and their statistically biased appearance An additional reason is due to the specific usage of synonymous codons depending on the nature of genes and their products as discussed by Ikemura.5 Furthermore, structural constraints within various regions of proteins encoded by respective genes are also conceivable factors affecting the statistical biases mentioned above Based on these considerations, we investigated whether or not the mitochondrial ribosomal protein (MRP) genes of the budding yeast Saccharomyces cerevisiae could be identified as genes in which characteristic appearance of stretches of nucleotide would be different from other yeast genes It has been postulated that mitochondria are descended from bacteria-like organisms that began to be associated with eukaryotic cells as endosymbionts and have since become specialized organella in the course of evolution A number of experimental data suggest that Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 Abstract The nucleotide sequence data for yeast mitochondrial ribosomal protein (MRP) genes were analyzed by the computer program GeneMark which predicts the presence of likely genes in sequence data by calculating statistical biases in the appearance of consecutive nucleotides The program uses a set of standard sequence data for this calculation We used this program for the analysis of yeast nucleotide sequence data containing MRP genes, hoping to obtain information as to whether they share features in common that are different from other yeast genes Sequence data sets for ordinary yeast genes and for 27 known MRP genes were used The MRP genes were nicely predicted as likely genes regardless of the data sets used, whereas other yeast genes were predicted to be likely genes only when the data set for ordinary yeast genes was used The assembled sequence data for chromosomes II, III, VIII and XI as well as the segmented data for chromosome V were analyzed in a similar manner In addition to the known MRP genes, eleven ORF's were predicted to be likely MRP genes Thus, the method seems very powerful in analyzing genes of heterologous origins Key words: yeast; mitochondrial ribosomal proteins; genomic sequence data; computer prediction [Vol 1, Prediction of Yeast Mito-Ribosomal Protein Genes 264 Table Sequences used for MRP-matrix file construction*) Accesion number ' X73673 X58362 X53840 X53841 X65014 X55977 M81696 M81697 M82841 S77888 Z25464 X69480 X15099 X56106 X17540 X17552 M15160 M22109 M15161 M22116 D90217 MRP gene MRP-L13 MRP17 MRP-L20 MRP-L8 MRP-L9 MRP-S28 MRP20 MRP49 MRP4 MRP-L27 MRP8 MRP-L6 MRP-L31 YMR26 YMR31 YMR44 MRP1 MRP13 MRP2 MRP7 MRP-L33 SCYBL038W SCYBR122C SCYBR146W SCYBR251W SCYBR268W SCYKL170W Z35799 Z35991 Z36015 Z36120 Z36137 Z28169 MRP-L16 MRP-L36 MRP-S9 MRP-S5 MRP-L37 MRP-L38 Length Chromosome 828 bp XI 396 588 717 810 861 791 414 XI XI X VII or XV Homologyc) - L17, S13 1,116 XVI 300 XIII L3 S15 S2 L6 S14 L27 L30 699 591 837 924 318 414 II II II II II XI L16 S9 S5 L14 1,185 441 660 618 393 474 372 297 966 975 348 ? ? XI VIII X XI VIII XI VII or XV VI XIII or XVI IV ? Reference 8, 32 8, 17 8, 18 19 31 20 26 8, 34 10, 27 30 8, 17 10, 21 8, 19 22 23 33 24 25 35 28 29 9 9 a) Two alternative initiation codons are assigned in YSCMRP20A for the protein coding region of MRP20, which result in ORF's of 791 and 762 bp, respectively The former was adopted in our calculation Also, the intron sequence (149 bp) included in the gene YMR44 has been omitted The six bottom sequences were included later (see text) b ^ Only the primary accession number of each sequence is listed c ' Homology to E coli ribosomal protein genes is shown - : No similarity was found with any known ribosomal protein genes many of the MRP's of S cerevisiae are very similar to the ribosomal proteins of E coli Their genes are, however, not present in the mitochondrial genome Instead, almost all of them reside in the nucleus, suggesting the transfer of MRP genes from the original mitochondrial genome to the nuclear genome during the course of evolution (for review see ref 6) The only MRP gene that is located in the mitochondrial genome of S cerevisiae is a gene termed VAR1.7 This is to indicate that the yeast genome, and perhaps other eukaryotic genomes, are likely to contain genes and their surrounding sequences derived from two or more origins Therefore, it might be that such imported segments are different in their characteristic appearance of consecutive nucleotides from the original chromosomal nucleotide sequence Below, we will show that at least such is the case for the MRP genes of yeast Materials and Methods The computer program GeneMark (previously, the program was named GENMARK; see ref 1) has been modified, and used in a SUN SparcStation with SUN 4.1 operating system, or more recently, in a SUN SparcStation 20 with Solaris 2.3 operating system As the standard matrix sequences for training the program, nucleotide sequence data containing 21 known MRP genes were collected from the GenBank nucleotide sequence database (release 85.0) as well as from the complete sequence for chromosome XI that was obtained from the EMBL ftp site (ftp.embl-heidelberg.de) An order four GeneMark matrix (MRP-mat.4) was constructed from a collection of protein-coding sequences by using the program AM AT (Borodovsky and Mclninch, unpublished) An order five matrix was also prepared using the same data set and termed MRP-mat.5 Both matrices were used in subsequent analysis The GenBank LOCUS Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 LOCUS name SCMRP SCMRP17 SCMRPL20 SCMRPL8 SCMRPL9G SCMRPS28 YSCMRP20A YSCMRP49A YSCMRP4A S77888 SC82KBXIA SCMTRPL6 SCMRPL31 SCYMR26 SCYMR31 SCYMR44 YSCMRP1 YSCMRP13 YSCMRP2A YSCMRP7 YSCYML33 No 6] K Isono, J D Mclninch, and M Borodovsky statistic characteristics in these MRP genes are not very much conflicting with each other However, since the five MRP genes on chromosome II were not predicted as highly likely genes when the old matrices, MRP-mat.4 and MRP-mat.5, were used, it is likely either that the MRP genes of yeast are not very homogeneous as far as the statistic characteristics detected by GeneMark are concerned, or that the number of genes whose nucleotide sequence data were incorporated into the matrix files was too small for statistically meaningful calculation We then performed similar analysis of the nucleotide sequence data for chromosomes III, VIII, and XI that were assembled into one contiguous sequence and became recently available In addition, the nucleotide sequence data for several large segments of chromosome V were also analyzed For these analyses, we used the MRP- and yeast genomic-matrices mentioned above All genes that had been assigned as MRP genes were nicely predicted as highly likely genes A typical example of the analysis is presented in Fig In this example, a region of chromo3 Results and Discussion some XI containing one of the MRP genes termed MRPThe gene has been assigned to ORF 3.1 Analysis with GeneMark of the nucleotide sequence was analyzed It is preceded by two nuclear genes, an RNA YKL142w data for chromosomes II, III, V, VIII and XI polymerase II PRB1 homolog (ORF YKL144c) and the The MRP-mat.4 (order 4) and MRP-mat.5 (order 5) LTV1 gene (encoding a low temperature viability promatrices were constructed as described in Materials and tein; ORF YKL143w), and followed by the SDH3 gene Methods and used to analyze the nucleotide sequence (encoding a succinate dehydrogenase; ORF YKL141w) as data of the three yeast chromosomal sequence data that have recently become available In addition, the data for indicated All four genes were predicted to be likely genes chromosomes III and V were extracted from the Gen- when the sc_cul.5 (order 5) matrix was used (Fig la) In Bank database and analyzed In the annotation lines contrast, when the MRP-matrices were used, only MRP8 to the chromosome II sequence data, five mitochondrial was nicely predicted as likely genes, but ORF's YKL144c protein genes, MRP-S5, MRP-S9, MRP-L27, MRP-L36 and YKL141w were not predicted to be likely genes at and MRP-L37, are assigned to ORF's, termed YBR251w, all (Fig lb) Interestingly, the likelihood prediction usYBR146w, YBR282w, YBR122c and YBR268w, respec- ing the MRP-27 mat matrix for ORF YKL143w (the tively In addition, ORF YBL038w has been assigned, LTV1 gene) was quite high except for the middle portion, though less strongly, to the gene MRP-L16 Among these although the protein encoded by this gene did not show ORF's, however, only the one for MRP-L27was detected a significant degree of similarity to any MRP genes nor as a highly likely MRP-gene by running program Gene- to any other mitochondrial protein genes Mark against the chromosome II sequence data in conIn addition to the known MRP genes, there were eleven junction with MRP-mat.4 and MRP-mat.5 All other ORF's that were predicted as likely MRP genes by GenMRP-ORF's were detected, but much less significantly eMark in the nucleotide sequence data for chromosomes Since the sequence data for MRP-L21 was previously II, III, V, VIII and XI In most cases, the likelihood probavailable under the LOCUS name of S77888 as listed ability was very high However, none of the ORF's dein Table 1, we suspected that the number of genes and tected in this way showed a significant degree of similarhence the cumulative length of sequences we used for ity to known ribosomal protein genes of prokaryotic as the construction of MRP-matrix files were not sufficient well as eukaryotic origins It is not surprising, because Therefore, we included the data for the genes on chro- many yeast MRP genes showed no significant similarmosome II and constructed new matrices A total of ity to any known ribosomal protein genes Among the 27 MRP genes were thus incorporated into the new ma- mitochondrial ribosomal protein genes of S cerevisiae, trices as shown in Table Accordingly, the new ma- there are as many as 13 out of 20 genes (65%) that trices were named MRP-27-mat.4 (order 4) and MRP- not posses apparent similarity to any known ribosomal 27-mat.5 (order 5) By using the two new matrices, we protein genes of other organisms.6 The ORF's that were were able to detect all the MRP genes on chromosome predicted to be likely MRP genes by GeneMark could II as highly likely genes This is to indicate that the thus be additional examples of this category, although with these data alone, it is difficult to decide whether Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 names and accession numbers of the nucleotide sequence data for MRP genes and the lengths of protein-coding regions including the translational terminators that were incorporated into these matrices are listed in Table The yeast nuclear gene matrix, sc_cul.5 prepared by Borodovsky and Mclninch (unpublished) was used for the prediction of other nuclear genes Results obtained by running GeneMark were visualized and analyzed by the SUN Openwindow-bundled tool Page View Recently, the sequence data for the entire chromosome XI have become available,8 along with the assembled nucleotide sequence data for chromosome II.9 The data were obtained from the ftp site at the Sanger Centre (ftp.sanger.ac.uk) Similarly, the assembled data for chromosome VIII10 were obtained from the ftp site at the Stanford University (genome-ftp.stanford.edu) The data for chromosome III11 as well as the segmental data for chromosome V were taken from the GenBank database 265 [Vol 1, Prediction of Yeast Mito-Ribosomal Protein Genes 266 VMMCKXI: CHRlW Wi-98 Nucleotide Position Y«t*Ch>.XJ: MRP nun-onMr uwd VKL142W: UftPS YKL143W: LTV) YKL141W: SDH3 Si 177B40 176192 178544 Nuclootioo Position Figure GeneMark prediction of likely genes in a region of chromosome XI A stretch of chromosome XI nucleotide sequence data (nucleotides 176,080 through 180,304) was analyzed with GeneMark in conjunction with the nuclear matrix sc-cul.5 (a) and MRP-27mat,4 (b) Four ORF's (YKL144c, YKL143w, YKL142w and YKL141w) were identified in this region as indicated ORF YKL142w (stippled) corresponds to the MRP8 gene.17 Ordinate indicates the likelihood probability and abscissa the nucleotide positions within the assembled sequence data Horizontal bars drawn at probability value of 0.5 indicate the positions and extent of ORF's Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 1778*0 No 6] K Isono, J D Mclninch, and M Borodovsky 267 R»fl1 -2 corrected Order * Window 96 SIBP 12 ** R»Ol-2 ongmat O d « ' « Window 96 S»C '2 l\ 99«SS 100020 Nucieotide Position M316 99*r9 100020 Nucieotide Position Figure GeneMark prediction of likely genes in a region of chromosome VIII A stretch of chromosome VIII nucieotide sequence data (nucleotides 98,612 through 100,724) was analyzed with GeneMark in conjunction with the MRP-27mat.4 matrix The original assembled sequence showed the existence of two highly likely MRP genes in this region (ORF-A and -B) that almost overlap each other (a) The corrected sequence, however, shows only one ORF as a highly likely MRP gene (b) they are indeed MRP genes that are not known till now Further analysis is needed to establish if they are indeed unidentified MRP genes or not We have attempted similar analysis of the MRP genes of other organisms There is only one case of MRP gene that is included in the current releases of GenBank (Release 85), EMBL (Release 40) and DDBJ (Release 19) databases, i.e the nucieotide sequence of an MRP gene, termed CYT-21, of Neurospora crassa stored under the LOCUS name of NCCYT21 (accession no X06360) The protein encoded by this gene shows similarity, though not of high degree, to E coli ribosomal protein S16.12 The gene was not detected as a likely gene by GeneMark with MRP-27-mat.4, however It is conceivable that the higher G+C content of N crassa genomic DNA (53.4%), including the CYT-21 gene, than that of S cerevisiae (38.3%), might be one of the major reasons for these results However, since no other MRP-gene sequences of N crassa are currently available, it is not possible to perform further comparison at the moment During the course of analysis of the nucieotide sequence data of chromosome VIII, we found that there is a region of the assembled nucieotide sequence data for this chromosome that contained the MRP4 gene The gene was assigned to ORF YHL004w (nucieotide positions at 99,213 through 100,397) of the assembled sequence data Upon analysis of the region containing this ORF with GeneMark and MRP-27mat.5, two likely genes (ORFA and -B) were recognized to exist in different reading frames as likely MRP genes that almost overlap each other as shown in Fig 2a No assignment was given to the second ORF in frame (ORF-B) Therefore, we examined the nucieotide sequence data for the MRP4 gene reported by Davis et al.13 and compared it with the assembled chromosome VIII sequence data It then became clear that the assembled sequence data of chromosome VIII (LOCUS SCCHRVIII; no accession number is available yet) contained an extra stretch of 40 bp at position 99,965 through 100,004 that is highly repetitive to the stretch immediately following it This 40 bp stretch does not exist in the sequence data, SC82KBXIA (accession number Z25464), reported by Davis et al.13 After eliminating this stretch from the assembled data, which resulted in the cumulative length of the assembled sequence to be 562,598 bp instead of 562,638 bp, we found that the GeneMark prediction pattern suggested the presence of only one ORF as a highly likely MRP gene (Fig 2b) Thus, the program is proven to be powerful to find sequence errors of this category as discussed by Kasai et al.3 Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 99318 268 Prediction of Yeast Mito-Ribosomal Protein Genes Acknowledgements: This work was supported in part by Grant-in-aid for scientific research from the Ministry of Education Nos 06261226 and 06558103 (to KI) and grant GM00783 from NIH (to MB and JDM) We are grateful to Showa-Hokokai (Osaka) and Kambara-Tosao Fund (Kobe University) for financial support References Borodovsky, M and Mclninch, J 1993, GENMARK: Parallel gene recognition for both DNA strands, Cornput Chem., 17, 123-133 Borodovsky, M., Koonin, Eu., and Rudd, K 1994, New genes in old sequences: A strategy for finding genes in a bacterial genome, Trends Biochem Sci., 19, 309-313 Kasai, H., Kim, S -O., Isono, S., Borodovsky, M., and Isono, K 1994, Solid phase nucleotide sequencing and its application to genome analysis of Escherichia coli K-12 In Advances in Biomagnetic Separation (Uhlen, M et al eds., Eaton Publishing), pp 113-125 Borodovsky, M., Rudd, K., and Koonin, Eu 1994, Intrinsic and extrinsic approaches for detecting genes in a bacterial genome, Nucl Acids Res., 22, 4756-4767 Ikemura, T 1981, Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E coli translational system, J Mol BioL, 151, 389-409 Kitakawa, M and Isono, K 1991, The mitochondrial ribosome, Biochimie, 73, 813-825 Hudspeth, M E S., Ainley, W M., Shumard, D S., Butow, R A., and Grossman, L I 1982, Location and structure of the varl gene on yeast mitochondrial DNA: Nucleotide sequence of the 40.0 allele, Cell, 30, 617-626 Dujon, B., Alexandraki, D., Andre B et al 1994, Complete DNA sequence of yeast chromosome XI, Nature, 369, 371-378 Feldmann, H., Aigle, M., Aljinovic, G et al 1994, Complete DNA sequence of yeast chromosome II (submitted) 10 Johnston, M., Andrews, S., Brinkman, R et al 1994, Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII, Science, 265, 2077-2082 11 Oliver, S G., Isono, K., Yoshikawa, A et al 1992, The complete DNA sequence of yeast chromosome III, Nature, 357, 38-46 12 Kuiper, M T R., Akins, R A., Holtrop, M., de Vries, H., and Lambowitz, A M 1988, Isolation and analysis of the Neurospora crassa CYT-21 gene: a nuclear gene encoding a mitochondrial ribosomal protein, J Biol Chem., 263, 2840-2847 13 Davis, S C , Tzagoloff, A., and Ellis, S R 1992, Characterization of a yeast mitochondrial ribosomal protein structurally related to the mammalian 68-kDa high affinity laminin receptor, J Biol Chem., 267, 5508-5514 14 Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Kohchi, T., Ogura, Y., Kanegae, T., Akashi, K., and Ohyama, K 1992, Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA, J Mol Biol., 223, 1-7 15 Takemura, M., Oda, K., Yamato, K., Ohta, E., Nakanuma, Y., Nozato, N., Akashi, K., and Ohyama, K 1992, Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marcantia polymorpha, Nucl Acids Res., 20, 3199-3205 16 Abraham, P R., Mulder, A., Van't Riet, J., Planta, R J., and Raue, H A 1992, Molecular cloning and physical analysis of an 8.2 kb segment of chromosome XI of Saccharomyces cerevisiae reveals five tightly linked genes, Yeast, 8, 227-238 17 Haffter, P and Fox, T D 1992, Suppression of carboxyterminal truncations of the yeast mitochondrial mRNAspecific translational activator PET122 by mutations in two new genes, MRP'17 and PET127, Mol Gen Genet, 235, 64-73 18 Kitakawa, M., Grohmann, L., Graack, H R., and Isono, K 1990, Cloning and characterization of nuclear genes for two mitochondrial ribosomal proteins in Saccharomyces cerevisiae, Nucleic Acids Res., 18, 1521-1529 19 Grohmann, L., Graack, H R., and Kitakawa, M 1989, Molecular cloning of the nuclear gene for mitochondrial ribosomal protein YmL31 from Saccharomyces cerevisiae, Eur J Biochem., 183, 155-160 Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 In the current databases, there are four entries that contain complete nucleotide sequences of mitochondria from plant and fungal species They include the data for the mitochondrial genome of the liverwort Marcantia polymorpha (MPOMTCG, accession no M68929), that is the only complete mitochondrial genome sequence of a plant species and is the longest of all mitochondrial genome sequences reported to date.14 The overall G+C content of this sequence is 42.4% and is slightly higher than that of the S cerevisiae genome (38.3%) There are sixteen ribosomal protein genes identified within the sequence data based on sequence similarity to those of the ribosomal protein genes of E coli.15 In contrast, the mitochondrial genomes of fungal as well as mammalian species, including that of S cerevisiae, contain no typical ribosomal protein gene In fact, the mitochondrial genomes of cerevisiae and a few other fungal species are known to contain only a single ribosomal protein gene, termed VAR1,7 that has no known counterpart in E coli and other bacteria We have performed GeneMark analysis of the liverwort mitochondrial genome with yeast MRP-matrices as well as with E coli matrices However, none of the fifteen ribosomal protein genes described were predicted to be likely genes Thus, although the genes encoded in the mitochondrial genome still retain sequence features with which their identification with those of E coli can be made, they not retain sequence characteristics with which their likelihood can be predicted by GeneMark in conjunction with either E coli- or with yeast MRP-matrices Further analyses are now in progress in which stretches of the yeast MRP gene sequences that are crucial for them to be identified as likely genes will be investigated [Vol 1, No 6] K Isono, J D Mclninch, and M Borodovsky 28 Fearon, K and Mason, T L 1988, Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP7, a protein of the large subunit of the mitochondrial ribosome, Mol Cell Biol., 8, 3636-3646 29 Kang, W -K., Matsushita, Y., Grohmann, L., Graack, H -R., Kitakawa, M., and Isono, K 1991, Cloning and analysis of the nuclear gene for YmL33, a protein of the large subunit of the mitochondrial ribosome in Saccharomyces cerevisiae, J Bacteriol, 173, 4013-4020 30 Graack, H R., Grohmann, and L., Kitakawa, M 1991, The nuclear coded mitoribosomal proteins YmL27 and YmL31 are both essential for mitochondrial function in yeast, Biochimie, 73, 837-844 31 Graack, H R., Grohmann, L., Kitakawa, M., Schafer, K L., and Kruft, V 1992, YmL9, a nucleus-encoded mitochondrial ribosomal protein of yeast, is homologous to L3 ribosomal proteins from all natural kingdoms and photosynthetic organelles, Eur J Biochem, 206, 373-380 32 Grohman, L., Kitakawa, M., Isono, K., GoldschmidtReisin, S., and Graack, H -R 1994, The yeast MRPL13 gene codes for a protein of the large subunit of the mitochondrial ribosome, Curr Genet., 26, 8-14 33 Matsushita, Y., Kitakawa, M., and Isono, K 1989, Cloning and analysis of the nuclear genes for two mitochondrial ribosomal proteins in yeast, Mol Gen Genet., 219, 119-124 34 Toda, T., Cameron, S., Sass, P., Zoller, M J., and Wigler, M 1987, Three different genes in S cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase, Cell, 50, 277-287 35 Myers, A M., Crivellone, M D., and Tzagoloff, A 1987, Assembly of the mitochondrial membrane system: MRP1 and MRP2, two yeast nuclear genes coding for mitochondrial ribosomal proteins, J Biol Chem., 262, 3388-3397 Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 20 Dang, H and Ellis, S R 1990, Structural and functional analysis of a yeast mitochondrial ribosomal protein homologous to ribosomal protein S15 of Escherichia coli, Nucleic Acids Res., 18, 6895-6901 21 Harrer, R., Schwank, S., Schueller, H J., and Schweizer, E 1993, Molecular cloning and analysis of the nuclear gene MRP-L6 coding for a putative mitochondrial ribosomal protein from Saccharomyces cerevisiae, Curr Genet., 24, 136-140 22 Kang, W K., Matsushita, Y., and Isono, K 1991, Cloning and analysis of YMR26, the nuclear gene for a mitochondrial ribosomal protein in Saccharomyces cerevisiae, Mol Gen Genet, 225, 474-482 23 Matsushita, Y., Kitakawa, M., and Isono, K 1989, Cloning and analysis of the nuclear genes for two mitochondrial ribosomal proteins in yeast, Mol Gen Genet., 219, 119-124 24 Myers, A M., Crivellone, M D., and Tzagoloff, A 1987, Assembly of the mitochondrial membrane system: MRP1 and MRP2, two yeast nuclear genes coding for mitochondrial ribosomal proteins, J Biol Chem., 262, 3388-3397 25 Partaledis, J A and Mason, T L 1988, Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP13, a protein of the small subunit of the mitochondrial ribosome, Mol Cell Biol., 8, 36473660 26 Fearon, K and Mason, T L 1992, Structure and function of MRP20 and MRP49, the nuclear gene for two proteins of the 54 S subunit of the yeast mitochondrial ribosome, J Biol Chem., 267, 5162-5170 27 Davis, S C , Tzagoloff, A., and Ellis, S R 1992, Characterization of a yeast mitochondrial ribosomal protein structurally related to the mammalian 68-kDa high affinity laminin receptor, J Biol Chem., 267, 5508-5514 269 Downloaded from http://dnaresearch.oxfordjournals.org/ at Wayne State University on March 29, 2015 ... is likely either that the MRP genes of yeast are not very homogeneous as far as the statistic characteristics detected by GeneMark are concerned, or that the number of genes whose nucleotide sequence... analysis of the MRP genes of other organisms There is only one case of MRP gene that is included in the current releases of GenBank (Release 85), EMBL (Release 40) and DDBJ (Release 19) databases,... XI containing one of the MRP genes termed MRPThe gene has been assigned to ORF 3.1 Analysis with GeneMark of the nucleotide sequence was analyzed It is preceded by two nuclear genes, an RNA YKL142w