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Oikonomou G, Machado VS, Santisteban C, Schukken YH, Bicalho RC. Microbial diversity of bovine mastitic milk as described by pyrosequencing of metagenomic 16s rDNA. PLoS One 2012; 7:e47671. [PMID: 23082192 PMCID: PMC3474744 DOI: 10.1371/journal.pone.0047671] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 09/18/2012] [Indexed: 11/20/2022] Open
Abstract
Dairy cow mastitis is an important disease in the dairy industry. Different microbial species have been identified as causative agents in mastitis, and are traditionally diagnosed by bacterial culture. The objective of this study was to use metagenomic pyrosequencing of bacterial 16S rRNA genes to investigate bacterial DNA diversity in milk samples of mastitic and healthy dairy cows and compare the results with those obtained by classical bacterial culture. One hundred and thirty-six milk samples were collected from cows showing signs of mastitis and used for microbiological culture. Additionally, 20 milk samples were collected from healthy quarters. Bacterial DNA was isolated from the same milk samples and the 16S rRNA genes were individually amplified and pyrosequenced. Discriminant analysis showed that the groups of samples that were most clearly different from the rest and thus easily discriminated were the normal milk samples from healthy cows and those characterised by culture as Trueperella pyogenes and Streptococcus spp. The mastitis pathogens identified by culture were generally among the most frequent organisms detected by pyrosequencing, and in some cases (Escherichia coli, Klebsiella spp. and Streptococcus uberis mastitis) the single most prevalent microorganism. Trueperella pyogenes sequences were the second most prevalent sequences in mastitis cases diagnosed as Trueperella pyogenes by culture, Streptococcus dysgalactiae sequences were the second most prevalent sequences in mastitis cases diagnosed as Streptococcus dysgalactiae by culture, and Staphyloccocus aureus sequences were the third most prevalent in mastitis cases diagnosed as Staphylococcus aureus by culture. In samples that were aerobic culture negative, pyrosequencing identified DNA of bacteria that are known to cause mastitis, DNA of bacteria that are known pathogens but have so far not been associated with mastitis, and DNA of bacteria that are currently not known to be pathogens. A possible role of anaerobic pathogens in bovine mastitis is also suggested.
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Affiliation(s)
- Georgios Oikonomou
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Vinicius Silva Machado
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Carlos Santisteban
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ynte Hein Schukken
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Rodrigo Carvalho Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Matsubara H, Sasaki RM, Chain RK. The amino Acid sequence of spinach ferredoxin. Proc Natl Acad Sci U S A 2010; 57:439-45. [PMID: 16591489 PMCID: PMC335525 DOI: 10.1073/pnas.57.2.439] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- H Matsubara
- SPACE SCIENCES LABORATORY AND DEPARTMENT OF CELL PHYSIOLOGY, UNIVERSITY OF CALIFORNIA, BERKELEY
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Greller LD, Erhan S. Short length amino acid sequence homology among ancestrally unrelated proteins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 2009; 6:165-73. [PMID: 4370369 DOI: 10.1111/j.1399-3011.1974.tb02375.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Morse DE, Horecker BL. The mechanism of action of aldolases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 31:125-81. [PMID: 4880215 DOI: 10.1002/9780470122761.ch4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Reeck GR, Teller DC. Sequence similarity betweenRhodospirillum rubrumribulose bisphosphate carboxylase/oxygenase and the large subunit of the plant enzyme. FEBS Lett 2001. [DOI: 10.1016/0014-5793(83)80889-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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MCLACHLAN A. Repeating Sequences and Gene Duplication in Proteins. Mol Biol 1989. [DOI: 10.1016/b978-0-12-131200-8.50034-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shapira SK, Finnerty VG. The use of genetic complementation in the study of eukaryotic macromolecular evolution: rate of spontaneous gene duplication at two loci of Drosophila melanogaster. J Mol Evol 1986; 23:159-67. [PMID: 3091844 DOI: 10.1007/bf02099910] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Gene duplications must play an important role in the evolutionary development of living organisms. Presented here is a general scheme that uses complementary alleles to isolate gene duplications in diploid organisms. The technique was used in Drosophila melanogaster to assess the rate of spontaneous gene duplication at two loci, maroon-like and rosy. The results indicate that the rate of duplication of the maroon-like locus is on the order of 2.7 X 10(-6); that the rate of duplication of the rosy locus is approximately 1.7 X 10(-4); and that duplication occurs in males, suggesting that there may actually be two modes of gene duplication in Drosophila melanogaster.
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Huh M, Friedhoff A. Multiple molecular forms of catechol-O-methyltransferase. Evidence for two distinct forms, and their purification and physical characterization. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)37918-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Yudkin MD. Unstable mutations that relieve catabolite repression of tryptophanase synthesis by Escherichia coli. J Bacteriol 1977; 130:57-61. [PMID: 323244 PMCID: PMC235173 DOI: 10.1128/jb.130.1.57-61.1977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
From strains of Escherichia coli that carry deletions of the trp region, five different mutants were isolated that were capable of synthesizing tryptophanase at unusually high rates in conditions of severe catabolite repression. Notwithstanding the comparative insensitivity to catabolite repression, the rates of tryptophanase synthesis in the mutants were greatly diminished by the introduction of a defective gene for adenyl cyclase. Each of the mutants segregated variants of the parental type. The results of genetic analysis appear to be consistent with the mutants arose by duplication of the tryptophanase gene.
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Sjödahl J. Repetitive sequences in protein A from Staphyloccus aureus: three highly homologous Fc-binding regions. FEBS Lett 1976; 67:62-7. [PMID: 955105 DOI: 10.1016/0014-5793(76)80871-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Zuckerkandl E. Evolutionary processes and evolutionary noise at the molecular level. II. A selectionist model for random fixations in proteins. J Mol Evol 1976; 7:269-311. [PMID: 180297 DOI: 10.1007/bf01743626] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
On account, notably, of a competition between different component functions for individual sites in polypeptide chains, each protein molecule represents a functional compromise, with some functions optimized, but the overall state of the molecule "suboptimal". The proposal is made that the selection coefficient relating to a protein molecule under given conditions can in principle be broken down into partial selection coefficients relevant to the different functions that the molecule carries out. At general-function sites, each fixation improves some function, while others deteriorate, at first nonsignificantly, and the overall adaptive state of the molecule fluctuates around its maximum. A selective mechanism is described whereby kaleidoscopic changes in primary structure at variable sites are indefinitely promoted, independently of any environmental changes and with the molecule remaining close to a state of maximal overall adaptation. The paradoxical aspect of this proposal is analyzed. The implication of specific functions in substitutions at general-function sites is noted. Further, it is shown that a certain category of changes in the internal environment of the organism can be integrated into the constant-environmental model for selection. Genetic sufficiency is considered a notion more adequate than genetic optimality for describing biological fitness and for providing a basis for the present model. On this basis selection occurs without genetic load. Multipolymorphism is one of the consequences. Several lines of evidence, in particular observations on polymorphism in deep sea organisms, seem to support the model. It is pointed out that it provides a theoretical foundation for a molecular evolutionary clock. The theoretical constancy of the clock depends on the constancy of functional density. The question of the evolution of functional density is examined. Comparisons of observed substitution frequencies with values expected on a random basis are rejected as a measure of the contribution to evolution of nondetermination. They are considered to reflect a hierarchy in the resistance of the molecules to different amino acid residues as substituents. A limited component of "true" randomness, again accompanied by selection, is on the other hand provided by the model. Most amino acid substitutions are considered evolutionary noise, even though noise compatible with selection. It is proposed that evolutionary significant substitutions may be identified by monitoring changes in functional density and weighted functional density.
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Abstract
The likelihood of a de novo generation of classes of efficient proteins through neoformation of DNA, through modification of expressed DNA, and through modification of nonexpressed DNA is examined. So is the likelihood that newly formed inefficient enzymes be turned into efficient enzymes. The conclusions are that neither gene duplicates nor dormant genes represent promising materials for a de novo generation of protein classes, that (with exceptions) such generation is unlikely to have taken place in recent evolution, that new structural genes must nearly consistently derive from preexisting structural genes, and that new functions can be evolved only on the basis of old proteins. Conditions of protein evolution in prokaryotes suggest that the saltatory formation of protein classes is as unlikely in prokaryotes as in eukaryotes. Data on the history of a few protein classes are reviewed to illustrate the preceding inferences. The analysis leads to the hypothesis that most protein classes originated before the major elements of the translation apparatus of modern cells were fully evolved. If simple sequence DNA is turned into structural genes by evolution, this process (again with exceptions) is considered to have taken place only at that very remote period. A polyphyletic origin of proteins is thought to date back to the same era. It is proposed that the development of genic multiplicity and of marked structural and functional diversity of proteins may have come about in the earliest cells primarily through the independent generation of structurally different polymerases in different protocells, followed by cell conjugation and the subsequent use by enriched cells of supernumerary types of polymerase for evolving further functions. Functional growth, as it took place at early times, is briefly discussed as well as functional change. The foundations for new functional developments in old proteins are analyzed. In considering the evolutionary recovery of lost functions, aspects of cell differentiation and gene regulation are linked with the evolutionary picture. The distinction between eurygenic and stemogenic control of gene activity is used. Next to gene deletion, cell and tissue deletion is held to be an event of general evolutionary significance, through cell and tissue origination that presumably accompanies the restoration of a lost molecular function.
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Abstract
An extensive search for internal regularities in amino acid sequences has been made, using both the genetic code and the relative frequencies of amino acid alternatives in homologous proteins. The two methods give very similar results and strongly suggest the occurrence of significant linear and inverted repetitions (similar sequences of opposite polarity) in several proteins. A hypothesis is developed to explain the occurrence of such internal regularities in proteins. This hypothesis is based on a process of duplication of an ancestral loop in which a symmetrical arrangement of amino acid allows stabilization by interaction between the amino acid side chains.
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Markert CL, Shaklee JB, Whitt GS. Evolution of a gene. Multiple genes for LDH isozymes provide a model of the evolution of gene structure, function and regulation. Science 1975; 189:102-14. [PMID: 1138367 DOI: 10.1126/science.1138367] [Citation(s) in RCA: 359] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ambler RP, Wynn M. The amino acid sequences of cytochromes c-551 from three species of Pseudomonas. Biochem J 1973; 131:485-98. [PMID: 4352718 PMCID: PMC1177496 DOI: 10.1042/bj1310485] [Citation(s) in RCA: 146] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The amino acid sequences of the cytochromes c-551 from three species of Pseudomonas have been determined. Each resembles the protein from Pseudomonas strain P6009 (now known to be Pseudomonas aeruginosa, not Pseudomonas fluorescens) in containing 82 amino acids in a single peptide chain, with a haem group covalently attached to cysteine residues 12 and 15. In all four sequences 43 residues are identical. Although by bacteriological criteria the organisms are closely related, the differences between pairs of sequences range from 22% to 39%. These values should be compared with the differences in the sequence of mitochondrial cytochrome c between mammals and amphibians (about 18%) or between mammals and insects (about 33%). Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50015 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973), 131, 5.
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McLachlan AD. Gene duplication in carp muscle calcium binding protein. NATURE: NEW BIOLOGY 1972; 240:83-5. [PMID: 4508373 DOI: 10.1038/newbio240083a0] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Gibbs AJ, McIntyre GA. The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 16:1-11. [PMID: 5456129 DOI: 10.1111/j.1432-1033.1970.tb01046.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Needleman SB, Blair TT. Homology of Pseudomonas cytochrome c-551 with eukaryotic c-cytochromes. Proc Natl Acad Sci U S A 1969; 63:1227-33. [PMID: 5260924 PMCID: PMC223454 DOI: 10.1073/pnas.63.4.1227] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The homology of Pseudomonas cytochrome c-551 with eukaryotic cytochromes c is examined with a computer-based procedure devised to determine whether similarities exist between these proteins. One method is given by which the more recently evolved cytochromes c might have arisen from the Pseudomonas protein. This procedure involves only common genetic phenomena and accounts for most of the structural differences between the bacterial and mammalian cytochromes. A time-scale relationship between the c-cytochromes from several microorganisms, a mold, yeast, and the eukaryotic organisms is proposed.
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Urbain J. Evolution of immunoglobulins and ferredoxins and the occurrence of pseudosymmetrical sequences. Biochem Genet 1969; 3:249-69. [PMID: 5409406 DOI: 10.1007/bf00521141] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Black JA, Dixon GH. Evolution of protamine: a further example of partial gene duplication. Nature 1967; 216:152-4. [PMID: 6057221 DOI: 10.1038/216152a0] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Epstein CJ. Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature 1967; 215:355-9. [PMID: 4964553 DOI: 10.1038/215355a0] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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