 Put2 and Ser3 (#1) |
| Description |
Ser3 (YER081W), D-3-Phosphoglycerate Dehydrogenase I, is involved in synthesis of serine from 3-phosphoglycerate. Serine can be formed from intermediates from both glycolysis via phosphorylated intermediates, from glycine formed from intermediates from tricarboxylic acid cycle intermediates (Ulane and Ogur 1971), and possibly from a third pathway (Melcher and Entian, 1992). Conditional auxotrophy was found in yeast strains in which growth requirements were exhibited under one set of conditions but not under other conditions, due to blockage of the primary biosynthetic pathway (Ulane and Ogur 1971). This suggests that other pathways to a given metabolite provide a possible escape from the limitations of just one pathway in case of a mutation (Ulane and Ogur 1971). The glycolytic pathway to serine formation begins with 3-phosphyglycerate and is under the regulation of amino-acid biosynthesis and serine repression (Melcher 1991).
Put2 (YHR037W), Delta-1-pyrroline-5-Carboxylate Dehydrogenase, carries out the second step in proline degradation of the conversion of proline to glutamate for use as a nitrogen source (Brandriss 1983 and Krzywicki and Brandriss, 1984). Lundgren and Ogur (1973) demonstrated proof of the conversion of proline to glutamate. They also demonstrated the inhibition of Delta-1-pyrroline-5-Carboxylate Dehydrogenase by serine (and other amino acids ) in the conversion of proline to glutamate (Lundgren and Ogur, 1973).
In both glutamate synthesis from proline degradation (via Put2) and serine biosynthesis (via Ser3), single mutations in the primary pathways produce auxotrophy due to tight regulation of secondary metabolic pathways by amino acid biosynthesis inhibition or catabolite repression (Lundgren and Ogur, 1973). Therefore, it is possible that some genetic mutations can be circumvented by the use and regulation of exisiting secondary pathways (Lundgren and Ogur, 1973). The profiles of Put2 and Ser3 show very high correlation as an inverted relationship, as shown in Figure ****. In the light of amino acid degradation and biosynthesis pathway intermediates overlapping and regulation, it is possible that they are biologically related by such pathway relationships, interactions, or control as suggested by Lundgren and Ogur (1973). Even though a direct inhibition and regulation has not been demonstrated in the literature between Put2 and Ser3, their highly correlated profiles and scientific background suggests such an inhibitory regulation mechanism exists between these two enzymes.
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| Reference |
Lundgren, D. W., and Ogur, M. Inhibition of yeast 1 -pyrroline-5-carboxylate dehydrogenase by common amino acids and the regulation of proline catabolism. Biochim Biophys Acta 297, 246-57 (1973).
Brandriss, M. C. Proline utilization in Saccharomyces cerevisiae: analysis of the cloned PUT2 gene. Mol Cell Biol 3, 1846-56 (1983).
Krzywicki, K. A., and Brandriss, M. C. Primary structure of the nuclear PUT2 gene involved in the mitochondrial pathway for proline utilization in Saccharomyces cerevisiae. Mol Cell Biol 4, 2837-42 (1984).
Melcher, K., and Entian, K. D. Genetic analysis of serine biosynthesis and glucose repression in yeast. Curr Genet 21, 295-300 (1992).
Ulane, R. and Ogur, M. Genetic and physiological control of serine and glycine biosynthesis in Saccharomyces. J. Bacteriol. 109:34-43 (1972).
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| YME1/YNT20 (#405) |
| Description |
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Yme genes were found when looking for mitochondrial DNA escape genes (DNA that escaped from the mitochondria and migrated to the nucleus). Yme1 is an ATP and metal-dependent protease associated with the inner mitochondrial membrane as part of a larger complex of proteins that are through to control the assembly and degradation of multisubunit protein complexes. Ynt20 has a mitochondrial targeting sequence, 3'-5' exonuclease motifs, a sequence element that can be cleaved in one step by the mitochondrial processing peptidase (MPP), and a motif typical for precursors cleaved in two steps by MPP and the mitochondrial intermediate peptidase (MIP). YNT20 is thereby thought to be a part of the Yme-1 mediated mitochondrial DNA escape pathway, such as by metabolism of RNA or mitochondrial DNA due to its 3'-5' exonuclease activity. [Hanekamp, 1999 #5].
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| ATF1 and MSF1 (#29) |
| ATF1 and MSF1 (#12) |
| Description |
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ATF1 is an alcohol acetyltransferase that catalyzes the condensation of acetyl-CoA to various alcohols to produce acetate esters (YPD). ATF1 has an inverted relationship with both MSF1 is a phenylanlanyl-tRNA synthetase, and MSY1 a tyrosyl-tRNA synthetase.(YPD)
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| SER3 (YER081W) and MSF1 (#23) |
| Description |
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Ser3 (YER081W), D-3-Phosphoglycerate Dehydrogenase I, is involved in synthesis of serine from 3-phosphoglycerate. MSF1 is a phenylanlanyl-tRNA synthetase. (YPD).
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| GAL11 has an inverted relationship with many mitochondrial proteins (see below) |
| GAL11 and MRPL10 (#51) |
| Description |
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GAL11 is a Component of RNA polymerase II holoenzyme and Kornberg's mediator complex with positive and negative effects on transcription. MRPL10 is a mitochondrial ribosomal protein of the large subunit, as well as a member of the L15 family of prokaryotic ribosomal proteins. (YPD)
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| GAL11 and NDE1 (#1806) |
| Description |
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GAL11 is a Component of RNA polymerase II holoenzyme and Kornberg's mediator complex with positive and negative effects on transcription. NDE1 is Mitochondrial NADH dehydrogenase that catalyzes cytosolic NADH oxidation
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| GAL11 and RPN2 (#2520) |
| Description |
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GAL11 is a Component of RNA polymerase II holoenzyme and Kornberg's mediator complex with positive and negative effects on transcription
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| GAL11 and RPN8 (#409) |
| Description |
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GAL11 is a Component of RNA polymerase II holoenzyme and Kornberg's mediator complex with positive and negative effects on transcription
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| GAL11 and RPT3 (#2791) |
| Description |
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GAL11 is a Component of RNA polymerase II holoenzyme and Kornberg's mediator complex with positive and negative effects on transcription
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| GAL11 and RPT4 (#2678) |
| Description |
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GAL11 is a Component of RNA polymerase II holoenzyme and Kornberg's mediator complex with positive and negative effects on transcription
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| GAL11 and YM9375.03 (#2922) |
| Description |
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GAL11 is a Component of RNA polymerase II holoenzyme and Kornberg's mediator complex with positive and negative effects on transcription. YM9375.03 is a mitochondrial NADH dehydrogenase that catalyzes cytosolic NADH oxidation
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| AD53 and 02333 (#1014) |
| RAD27 and 02333 (#1209) |
| Description |
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02333 (YOL014W) is a protein of unknown function (YPD). RAD53 is a serine/threonine/tyrosine protein kinase with a checkpoint function in S and G2 phases that acts to prevent mitosis from occurring in cells with DNA damage or with unreplicated DNA (YPD) RAD27 is a single-stranded DNA endonuclease and 5'-3' exonuclease that functions in the MSH2-MLH1-PMS1-dependent mismatch repair system. Its inverted profile relationship with RAD53 and RAD27 suggests that it could be involved in the inhibition, or is inhibited by, these DNA repair and checkpoint mechanisms.
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| RAD54 and CDC20 (#1254) |
| Description |
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RAD54 is a DNA-dependent ATPase of the Snf2p family that is required for mitotic recombination and DNA repair of X-ray damage (YPD). CDC20 is required for microtubule function during mitosis and for exiting anaphase. (YPD)
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| N1909 (YNL120C) has an inverted relationship with many ribosomal proteins |
| N1909 is a protein of unknown function, is an internal ORF to TOM70 |
| N1909 and RPL11B |
| Description |
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Ribosomal protein L7 (yeast L6; YL8B; rp11; E. coli L30; rat L7), nearly identical to Rpl7Ap
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| N1909 and RPL22A
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| Description |
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Ribosomal protein L22, similar to Rpl22Bp
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| N1909 and RPL31B
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| Description |
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Ribosomal protein L31 (yeast L34; YL36; YL28; rat L31), nearly identical to Rpl31Ap
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| N1909 and RPL33A
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| Description |
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Ribosomal protein L33 (yeast L37; YL37; rp47; rat L35A), nearly identical to Rpl33Bp
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| N1909 and RPL33B
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| Description |
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Ribosomal protein L33 (yeast L37; YL37; rp47; rat L35A), nearly identical to Rpl33Ap
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| N1909 and RPL34B
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| Description |
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Ribosomal protein L34 (rat L34), nearly identical to Rpl34Ap
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| N1909 and RPL37A
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| Description |
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Ribosomal protein L37 (yeast L46; rat L37), nearly identical to Rpl37Bp
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| N1909 and RPL38
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| Description |
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Ribosomal protein L38
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| N1909 and RPL40B
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| Description |
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Fusion protein comprised of ribosomal protein L40 (C-terminal half) and ubiquitin (N-terminal half), (rat L40), identical to Rpl40Ap
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| N1909 and RPL7B
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| Description |
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Ribosomal protein L7 (yeast L6; YL8B; rp11; E. coli L30; rat L7), nearly identical to Rpl7Ap
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| N1909 and RPS1A
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| Description |
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Ribosomal protein S1 (rp10; rat S3A), nearly identical to Rps1Bp
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| N1909 and RPS28A
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| Description |
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Ribosomal protein S28 (yeast S33; YS27; mammalian S28), nearly identical to Rps28Bp
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| N1909 and RPS3
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| Description |
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Ribosomal protein S3 (rp13; YS3; mammalian S3), has a possible KH domain
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| N1909 and RPS30B
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| Description |
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Ribosomal protein S30B (mammalian S30), identical to Rps30Ap
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| N1909 and RPS31
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| Description |
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usion protein comprised of ribosomal protein S31 at the C-terminal half fused to ubiquitin at the N-terminal half (yeast S37;YS24; rat S27a)
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| SMK1 has an inverted relationship to many ribosomal proteins |
| SKM1 is a sporulation-specific protein kinase (MAP family) that is required for completion of sporulation (YPD) |
| SMK1 and PDC1
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| Description |
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Pyruvate decarboxylase isozyme 1
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| SMK1 and RPL10
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| Description |
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Ribosomal protein L10 (yeast L9)
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| SMK1 and RPL11A
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| Description |
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Ribosomal protein L11 (yeast L16; YL22; rp39A; E. coli L5; rat L11), nearly identical to Rpl11Bp
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| SMK1 and RPL22A
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| Description |
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Ribosomal protein L22, similar to Rpl22Bp
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| SMK1 and RPL33B
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| Description |
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Ribosomal protein L33 (yeast L37; YL37; rp47; rat L35A), nearly identical to Rpl33Ap
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| SMK1 and RPL38
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| Description |
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Ribosomal protein L38
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| SMK1 and RPL7A
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| Description |
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Ribosomal protein L7 (yeast L6; YL8A; rp11; E. coli L30; rat L7), nearly identical to Rpl7Bp
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| SMK1 and RPS1A
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| Description |
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Ribosomal protein S1 (rp10; rat S3A), nearly identical to Rps1Bp
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| SMK1 and RPS1B
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| Description |
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Ribosomal protein S1 (rp10; rat S3A), nearly identical to Rps1Ap
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| SMK1 and RPS21A
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| Description |
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Ribosomal protein S21 (yeast S26; YS25; rat S21), identical to Rps21Bp
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| SMK1 and RPS22B
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| Description |
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RIbosomal protein S22 (yeast S24; rp50; YS22; rat S15A), nearly identical to Rps22Ap
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| SMK1 and RPS28A
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| Description |
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Ribosomal protein S28 (yeast S33; YS27; mammalian S28), nearly identical to Rps28Bp
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| SMK1 and RPS30B
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| Description |
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Ribosomal protein S30B (mammalian S30), identical to Rps30Ap
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| SMK1 and RPS31
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| Description |
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Fusion protein comprised of ribosomal protein S31 at the C-terminal half fused to ubiquitin at the N-terminal half (yeast S37)
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| SMK1 and RPS5
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| Description |
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Ribosomal protein Rps5p (rp14; YS8; S2; mammalian S5) of the small subunit
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