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Kobayashi CR, Castillo-González C, Survotseva Y, Canal E, Nelson ADL, Shippen DE. Recent emergence and extinction of the protection of telomeres 1c gene in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:1081-1097. [PMID: 31134349 PMCID: PMC6708462 DOI: 10.1007/s00299-019-02427-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/27/2019] [Indexed: 05/20/2023]
Abstract
Duplicate POT1 genes must rapidly diverge or be inactivated. Protection of telomeres 1 (POT1) encodes a conserved telomere binding protein implicated in both chromosome end protection and telomere length maintenance. Most organisms harbor a single POT1 gene, but in the few lineages where the POT1 family has expanded, the duplicate genes have diversified. Arabidopsis thaliana bears three POT1-like loci, POT1a, POT1b and POT1c. POT1a retains the ancestral function of telomerase regulation, while POT1b is implicated in chromosome end protection. Here we examine the function and evolution of the third POT1 paralog, POT1c. POT1c is a new gene, unique to A. thaliana, and was derived from a duplication event involving the POT1a locus and a neighboring gene encoding ribosomal protein S17. The duplicate S17 locus (dS17) is highly conserved across A. thaliana accessions, while POT1c is highly divergent, harboring multiple deletions within the gene body and two transposable elements within the promoter. The POT1c locus is transcribed at very low to non-detectable levels under standard growth conditions. In addition, no discernable molecular or developmental defects are associated with plants bearing a CRISPR mutation in the POT1c locus. However, forced expression of POT1c leads to decreased telomerase enzyme activity and shortened telomeres. Evolutionary reconstruction indicates that transposons invaded the POT1c promoter soon after the locus was formed, permanently silencing the gene. Altogether, these findings argue that POT1 dosage is critically important for viability and duplicate gene copies are retained only upon functional divergence.
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Affiliation(s)
- Callie R Kobayashi
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | | | - Yulia Survotseva
- Yale Center for Molecular Discovery, Yale University, New Haven, Connecticut, USA
| | - Elijah Canal
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Andrew D L Nelson
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dorothy E Shippen
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
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2
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Coetzee MPA, Wingfield BD, Coutinho TA, Wingfield MJ. Identification of the causal agent of Armillaria root rot of Pinus species in South Africa. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Martin P. A. Coetzee
- Department of Genetics, Tree Pathology Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Brenda D. Wingfield
- Department of Genetics, Tree Pathology Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Teresa A. Coutinho
- Department of Microbiology and Plant Pathology, Tree Pathology Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Michael J. Wingfield
- Department of Genetics, Tree Pathology Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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3
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Dharia AP, Obla A, Gajdosik MD, Simon A, Nelson CE. Tempo and mode of gene duplication in mammalian ribosomal protein evolution. PLoS One 2014; 9:e111721. [PMID: 25369106 PMCID: PMC4219774 DOI: 10.1371/journal.pone.0111721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/06/2014] [Indexed: 12/17/2022] Open
Abstract
Gene duplication has been widely recognized as a major driver of evolutionary change and organismal complexity through the generation of multi-gene families. Therefore, understanding the forces that govern the evolution of gene families through the retention or loss of duplicated genes is fundamentally important in our efforts to study genome evolution. Previous work from our lab has shown that ribosomal protein (RP) genes constitute one of the largest classes of conserved duplicated genes in mammals. This result was surprising due to the fact that ribosomal protein genes evolve slowly and transcript levels are very tightly regulated. In our present study, we identified and characterized all RP duplicates in eight mammalian genomes in order to investigate the tempo and mode of ribosomal protein family evolution. We show that a sizable number of duplicates are transcriptionally active and are very highly conserved. Furthermore, we conclude that existing gene duplication models do not readily account for the preservation of a very large number of intact retroduplicated ribosomal protein (RT-RP) genes observed in mammalian genomes. We suggest that selection against dominant-negative mutations may underlie the unexpected retention and conservation of duplicated RP genes, and may shape the fate of newly duplicated genes, regardless of duplication mechanism.
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Affiliation(s)
- Asav P. Dharia
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Ajay Obla
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Matthew D. Gajdosik
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Amanda Simon
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
| | - Craig E. Nelson
- University of Connecticut Department of Molecular and Cell Biology, Storrs, Connecticut, United States of America
- * E-mail:
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4
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Deep metazoan phylogeny: When different genes tell different stories. Mol Phylogenet Evol 2013; 67:223-33. [DOI: 10.1016/j.ympev.2013.01.010] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/08/2013] [Accepted: 01/12/2013] [Indexed: 11/30/2022]
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Warren AS, Anandakrishnan R, Zhang L. Functional bias in molecular evolution rate of Arabidopsis thaliana. BMC Evol Biol 2010; 10:125. [PMID: 20433764 PMCID: PMC2876160 DOI: 10.1186/1471-2148-10-125] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 05/01/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they are responsible for fundamental biological function, others are conserved for their unique functional characteristics. Therefore one would expect the rate of molecular evolution for individual genes to be dependent on their biological function. Whether this expectation holds for genes duplicated by whole genome duplication is not known. RESULTS We empirically demonstrate here, using duplicated genes generated from the Arabidopsis thaliana alpha-duplication event, that the rate of molecular evolution of genes duplicated in this event depend on biological function. Using functional clustering based on gene ontology annotation of gene pairs, we show that some duplicated genes, such as defense response genes, are under weaker purifying selection or under stronger diversifying selection than other duplicated genes, such as protein translation genes, as measured by the ratio of nonsynonymous to synonymous divergence (dN/dS). CONCLUSIONS These results provide empirical evidence indicating that molecular evolution rate for genes duplicated in whole genome duplication, as measured by dN/dS, may depend on biological function, which we characterize using gene ontology annotation. Furthermore, the general approach used here provides a framework for comparative analysis of molecular evolution rate for genes based on their biological function.
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Affiliation(s)
- Andrew S Warren
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
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6
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Lukashenko NP. Molecular evolution of ciliates (Ciliophora) and some related groups of protozoans. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409080018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Ohyanagi H, Ikeo K, Gojobori T. Eukaryotic nuclear structure explains the evolutionary rate difference of ribosome export factors. Gene 2008; 421:7-13. [DOI: 10.1016/j.gene.2008.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2007] [Revised: 03/04/2008] [Accepted: 05/21/2008] [Indexed: 10/22/2022]
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8
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Subacius SMR, Bussab WDO. Purine and pyrimidine composition in 5S rRNA and its mutational significance. Genet Mol Biol 1998. [DOI: 10.1590/s1415-47571998000200014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Variations observed in 5S rRNA base compositions are almost entirely due to fixation of point mutations. As a consequence, 5S rRNA size has remained relatively constant during evolution and, therefore, dependencies among the four bases can be predicted. In order to characterize the nature and to determine the degree of such dependencies, correlation analysis followed by principal component factorial analysis was conducted on a large sample of 5S rRNA sequences. The results show that the purine and pyrimidine contents tend to remain constant, so that A + G = Kpur and C + U = Kpyr. The composition of the four bases expressed now by Kpur/Kpyr relationships is also constant (Ks). These relationships imply that the behavior of the mutations in the variable sites of the molecule follows rules imposed by the chemical nature of the bases involved. Consequently, transition mutations would be more favored than substitutions in transversion sites and also than insertion-deletion (rare in 5S rRNAs), since transitions would not significantly alter the values of the Ks-index.
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Greenwood SJ, Sogin ML, Lynn DH. Phylogenetic relationships within the class Oligohymenophorea, phylum Ciliophora, inferred from the complete small subunit rRNA gene sequences of Colpidium campylum, Glaucoma chattoni, and Opisthonecta henneguyi. J Mol Evol 1991; 33:163-74. [PMID: 1840618 DOI: 10.1007/bf02193631] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Phylogenetic relationships within the class Oligohymenophorea, phylum Ciliophora, were investigated by determining the complete small subunit rRNA (SSrRNA) gene sequences for the hymenostomes Colpidium campylum, Glaucoma chattoni, and the peritrich Opisthonecta henneguyi. The affiliations of the oligohymenophoreans were assessed using both distance matrix (DM) and maximum parsimony (MP) analyses. Variations do exist in the phylogenies created by the two methods. However, the basic tree topologies are consistent. In both the DM and MP analyses the hymenostomes (C. campylum, G. chattoni, and the tetrahymenas) all form a very tight group associated with the peritrich O. henneguyi. The Tetrahymena lineage was monophyletic whereas Colpidium and Glaucoma were more closely related to each other than either was to the tetrahymenas. The monophyly of the genus Tetrahymena in the present analysis supports the phylogenies determined from morphological data and molecular sequence data from the histone H3II/H4II region of the genome. The perplexing and controversial phylogenetic position of the peritrichs is once again depicted in the present analysis. The distinctiveness of the peritrich Opisthonecta from both hymenostome and nassophorean ciliates based on evolutionary distances suggests that the elevation of the peritrichs to a higher taxonomic rank should be reconsidered.
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Affiliation(s)
- S J Greenwood
- Department of Zoology, University of Guelph, Ontario, Canada
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10
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Grundy FJ, Henkin TM. The rpsD gene, encoding ribosomal protein S4, is autogenously regulated in Bacillus subtilis. J Bacteriol 1991; 173:4595-602. [PMID: 1906866 PMCID: PMC208134 DOI: 10.1128/jb.173.15.4595-4602.1991] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Although the mechanisms for regulation of ribosomal protein gene expression have been established for gram-negative bacteria such as Escherichia coli, the regulation of these genes in gram-positive bacteria such as Bacillus subtilis has not yet been characterized. In this study, the B. subtilis rpsD gene, encoding ribosomal protein S4, was found to be subject to autogenous control. In E. coli, rpsD is located in the alpha operon, and S4 acts as the translational regulator for alpha operon expression, binding to a target site in the alpha operon mRNA. The target site for repression of B. subtilis rpsD by protein S4 was localized by deletion and oligonucleotide-directed mutagenesis to the leader region of the monocistronic rpsD gene. The B. subtilis rpsD leader exhibits little sequence homology to the E. coli alpha operon leader but may be able to form a pseudoknotlike structure similar to that found in E. coli.
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Affiliation(s)
- F J Grundy
- Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Shreveport 71130
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11
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Dekio S, Hashimoto K, Makino M. Two-dimensional gel electrophoresis of ribosomal proteins from Propionibacterium acnes and granulosum. ZENTRALBLATT FUR BAKTERIOLOGIE : INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY 1989; 271:442-51. [PMID: 2818796 DOI: 10.1016/s0934-8840(89)80103-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ribosomal proteins (r-proteins) from a type I strain (ATCC 11827) and a type II strain (ATCC 11828) of Propionibacterium acnes (P. acnes) and from a Propionibacterium granulosum (P. granulosum) strain (ATCC 11829-2) were analyzed using two-dimensional polyacrylamide gel electrophoresis (two-dimensional PAGE), for the purpose of genetical analysis of the P. acnes type I and type II strains and the P. granulosum strain. Among the fifty r-proteins in all, almost all of the proteins were electrophoretically different between both of the two types of P. acnes strains and the P. granulosum strain, whereas only five proteins were different between the type I and type II strains of P. acnes. Such differences of r-protein composition between the type I and type II strains of P. acnes indicate that the type I strain is genetically different from, but very closely related to, the type II strain. However, the P. granulosum strain is not so closely related to both the two types of P. acnes strains. This study thus suggests that the two-dimensional PAGE of r-proteins is an excellent tool for the taxonomy of P. acnes and the related bacteria.
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Affiliation(s)
- S Dekio
- Department of Dermatology and Syphilology, Wayne State University School of Medicine, Detroit, Michigan
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12
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Henkin TM, Moon SH, Mattheakis LC, Nomura M. Cloning and analysis of the spc ribosomal protein operon of Bacillus subtilis: comparison with the spc operon of Escherichia coli. Nucleic Acids Res 1989; 17:7469-86. [PMID: 2508062 PMCID: PMC334824 DOI: 10.1093/nar/17.18.7469] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A segment of Bacillus subtilis chromosomal DNA homologous to the Escherichia coli spc ribosomal protein operon was isolated using cloned E. coli rplE (L5) DNA as a hybridization probe. DNA sequence analysis of the B. subtilis cloned DNA indicated a high degree of conservation of spc operon ribosomal protein genes between B. subtilis and E. coli. This fragment contains DNA homologous to the promoter-proximal region of the spc operon, including coding sequences for ribosomal proteins L14, L24, L5, S14, and part of S8; the organization of B. subtilis genes in this region is identical to that found in E. coli. A region homologous to the E. coli L16, L29 and S17 genes, the last genes of the S10 operon, was located upstream from the gene for L14, the first gene in the spc operon. Although the ribosomal protein coding sequences showed 40-60% amino acid identity with E. coli sequences, we failed to find sequences which would form a structure resembling the E. coli target site for the S8 translational repressor, located near the beginning of the L5 coding region in E. coli, in this region or elsewhere in the B. subtilis spc DNA.
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Affiliation(s)
- T M Henkin
- Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Shreveport 71130
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13
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Smith HJ, Bourque DP. Species-specific proteins of the 50S subunit of the chloroplast ribosome in the genus Nicotiana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1985; 71:26-30. [PMID: 24247334 DOI: 10.1007/bf00278249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/1985] [Accepted: 03/25/1985] [Indexed: 06/02/2023]
Abstract
The large subunits (50S) of chloroplast ribosomes were isolated from Nicotiana tabacum, a species of the Western Hemisphere, and from N. excelsior and N. gossei, Australian species. Their proteins were compared by two-dimensional gel electrophoresis. A pair of proteins (T12 and T12) observed in N. tabacum has electrophoretic mobilities which differ from those of a similarly migrating, and probably homologous, pair of proteins observed in N. excelsior and N. gossei. The species-specific proteins in N. tabacum differ slightly in electrophoretic mobilities based on both charge and molecular weight from those in N. excelsior and N. gossei. Tryptic digests of radioiodinated proteins reveal that the peptide maps of all six proteins are similar. These results suggest that chemically altered forms of one or more proteins of the 50S chloroplast ribosome subunit may exist in vivo.
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Affiliation(s)
- H J Smith
- Department of Biochemistry, University of Arizona, 537 Biological Sciences West, 85721, Tucson, AZ, USA
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Higo K, Otaka E, Osawa S. Purification and characterization of 30S ribosomal proteins from Bacillus subtilis: correlation to Escherichia coli 30S proteins. MOLECULAR & GENERAL GENETICS : MGG 1982; 185:239-44. [PMID: 6806564 DOI: 10.1007/bf00330792] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Twenty proteins were isolated from the 30S ribosomal subunits of Bacillus subtilis and their amino acid compositions and amino-terminal amino acid sequences were determined. These results were compared with the data of Escherichia coli 30S ribosomal proteins and the structural correspondence of individual ribosomal proteins has been established between B. subtilis and E. coli. Post-translational modifications of amino-terminal amino acids of the ribosomal proteins which have been found in E. coli are almost absent in B. subtilis with the exception of acetylated forms of S9.
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15
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Tyagi S. Origins of translation: the hypothesis of permanently attached adaptors. ORIGINS OF LIFE 1981; 11:343-51. [PMID: 6799890 DOI: 10.1007/bf00931489] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A mechanism for prebiotic translation is proposed in which primeval transfer-RNA (adaptors) are assumed to be permanently associated with messenger nucleic acid molecules. Residual 'fossil' evidences are found to be present within the base sequences of contemporary tRNAs, suggesting the existence of inter-primal-tRNA interactions necessary for the mechanism. The structure of proposed primal-tRNA is such that it can not only choose its own amino acid in the absence of aminoacyl synthetase, but can also associate nonspecifically with adjacent primal-tRNA molecules attached to the neighbouring codons. Such associations can give rise, through cooperative binding between message and adaptors to the 'static template surfaces' which can direct translation of nucleotide sequences into those of amino acids. The origins of ribosomes and contemporary genetic code are suggested by this hypothesis. Proposed structures and processes are thermodynamically compatible. The approximate date of occurrence of the proposed system is calculated, which is consistent with the period of occurrence of the earliest organism with ribosomes.
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Svoboda AJ, McConkey EH. Identification of homologous ribosomal proteins in HeLa cells and in Tetrahymena pyriformis. A study of proteins binding 5-S RNA and acidic proteins released from 40-S subunits by EDTA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 116:397-402. [PMID: 6166475 DOI: 10.1111/j.1432-1033.1981.tb05348.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Tetrahymena pyriformis 60-S ribosomal subunits treated with EDTA release a 7-S particle containing 5-S RNA and a 36000-Mr protein that is similar to mammalian 5-S-RNA-binding protein L5 in molecular weight, in two-dimensional acrylamide gel mobility, and in peptide pattern as generated by a simple, one-dimensional acrylamide gel technique. Human and T. pyriformis 40-S ribosomal subunits, treated with buffers lacking magnesium or containing EDTA, release varying amounts of two large acidic proteins. We have identified these released proteins by two-dimensional gel electrophoresis.
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17
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Adoutte-Panvier A, Davies JE, Gritz LR, Littlewood BS. Studies of ribosomal proteins of yeast species and their hybrids: gel electrophoresis and immunochemical cross-reactions. MOLECULAR & GENERAL GENETICS : MGG 1980; 179:273-82. [PMID: 7007807 DOI: 10.1007/bf00425454] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The cytoplasmic ribosomal proteins (r-proteins) of seventeen yeast species of the genera Saccharomyces and Kluyveromyces were analyzed by one-dimensional gradient polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate. The electrophoretic patterns of cytoplasmic r-proteins from different species display extensive differences in both the 40S and the 60S subunit. Relatedness of species suggested by r-protein patterns correlates well with that based on DNA/DNA homology (Bicknell and Douglas 1970). Immunochemical cross-reactions and antibiotic susceptibility tests were also used to compare different species. Analyses of r-proteins from two different interspecific hybrids showed that their ribosomes were hybrid, containing r-proteins from both parents. These findings are discussed in relation to the evolution of yeast species and the regulation of expression of r-proteins in eucaryotes.
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Eladari ME, Hampe A, Galibert F. Comparative studies of the primary structures of ribosomal RNAs of several eukaryotic cell lines by the fingerprinting method. Biochimie 1980; 61:1097-12. [PMID: 119549 DOI: 10.1016/s0300-9084(80)80224-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Comparisons of the primary structures of 18S and 28S ribosomal RNAs of man, rat, mouse and chicken were made by two-dimensional fractionation including electrophoresis at pH 3.5 and homochromatography. All large T1 oligonucleotides were recovered from the different fingerprints and their radioactivity was measured. They were then hydrolysed with pancreatic RNase and the pancreatic products were digested with alkali to determine their base composition and detect modified residues. Finally, residues bearing a modification on the ribose were analysed by hydrolyses with snake venom and spleen phosphodiesterases. For the 18A RNAs 23, 27, 26, 24 oligonucleotides, whose lengths range from 22 to 10 residues, were analyzed respectively for man, rat, mouse and chicken. Among these, 14 are identical in the four species, two at least are common to man, rat, mouse but differ by the presence of A-Cps in chicken spot 4' instead of A-Up in spot 4 and A2-Gp in chicken spot 14 instead of A2-Gp in spot 13. For the 28S RNAs of man, rat, mouse and chicken, 20, 19, 21 and 22 oligonucleotides ranging in length from 27 to 12 residues were analyzed. 11 of them are common to the four species; 4 of them are found in man, rat, mouse and one of these (spot 1) has a corresponding spot in chicken from which it differs only by the existence of A3-Up instead of A2-Up. Another mammalian oligonucleotide (spot 6) differs from its homologous chicken spot (spot 6') bytwo point mutations. The same modified residues as found by Khan and Maden in man, chicken, and xenopus, have been found in rat and mouse. Moreover when these modified residues are common to several species they are found within an identical nucleotide sequence, as can be seen in the case of spots 1, 3, 9, 11 of 18S RNAs and 4, 7, 13 for 28S RNAs. The number of differences observed between the ribosomal RNAs of the four species were compared to the number of differences observed in the same species for several proteins, globins alpha and beta, insulin, cytochrome C and lysozyme.
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Abstract
The evolution of ribosomal proteins of about 70 bacterial strains belonging to the family Enterobacteriaceae has been studied by use of previously reported data (S. Osawa, T. Itoh, and E. Otaka, J. Bacteriol. 107:168-178, 1971) and those obtained in this paper. The proximity of the bacteria was quantified by co-chromatographing the differentially labeled ribosomal proteins from two strains on a column of carboxymethyl cellulose in various combinations. The were then classified into 12 groups (=species?) according to their ribosomal protein compositions and were placed in a phylogenic tree.
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