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1

Understanding the evolution of restriction-modification systems: Clues from sequence and structure comparisons

100%
Bujnicki J. M.
Acta Biochimica Polonica
|
2001
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tom 48
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nr 4
Restriction-modification (RM) systems comprise two opposing enzymatic activities: a restriction endonuclease, that targets specific DNA sequences and performs endonucleolytic cleavage, and a modification methyltransferase that renders these se­quences resistant to cleavage. Studies on molecular genetics and biochemistry of RM systems have been carried out over the past four decades, laying foundations for mod­ern molecular biology and providing important models for mechanisms of highly spe­cific protein-DNA interactions. Although the number of known, relevant sequences 3D structures of RM proteins is growing steadily, we do not fully understand their functional diversities from an evolutionary perspective and we are not yet able to en­gineer new sequence specificities based on rational approaches. Recent findings on the evolution of RM systems and on their structures and mechanisms of action have led to a picture in which conserved modules with defined function are shared between different RM proteins and other enzymes involved in nucleic acid biochemistry. On the other hand, it has been realized that some of the modules have been replaced in the evolution by unrelated domains exerting similar function. The aim of this review is to give a survey on the recent progress in the field of structural phylogeny of RM en­zymes with special emphasis on studies of sequence-structure-function relationships and emerging potential applications in biotechnology.
2

Artificially engineered specific nucleases - a breakthrough in RE research - Review

100%
Cesnaviciene E.
Biotechnologia
|
2003
|
nr 2
3

Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage

100%
Bujnicki J. M., Radlinska M., Zaleski P., Piekarowicz A.
Acta Biochimica Polonica
|
2001
|
tom 48
|
nr 4
In this paper we report cloning and experimental characterization of the DNA ade­nine methyltransferase (dam) gene from Haemophilus influenzae and comparison of its product with the Dam protein from the lysogenic phage of H. influenzae, HP1. Mo­lecular modeling of M.HinDam and M.HP1Dam was carried out, providing a frame­work for a comparative analysis of these enzymes and their close homologs in the structural context. Both proteins share the common fold and essential cofactor-bind- ing and catalytic residues despite overall divergence. However, subtle but significant differences in the cofactor-binding pocket have been identified. Moreover, while M.HinDam seems to contact its target DNA sequence using a number of loops, most of them are missing from M.HP1Dam. Analysis of both MTases suggests that their cata­lytic activity was derived from a common ancestor, but similar sequence specificities arose by convergence.
4

Molecular systematics: a synthesis of the common methods and the state of knowledge

84%
Mauro D. S., Agorreta A.
Cellular and Molecular Biology Letters
|
2010
|
tom 15
|
nr 2
The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.
5

Molecular evolution of coding and non-coding sequences of the growth hormone receptor [GHR] gene in the family Bovidae

84%
Maj A., Zwierzchowski L.
Folia Biologica
|
2006
|
tom 54
|
nr 1-2
6

The impact of research on parasites beyond parasitology

84%
Kohler P.
Acta Parasitologica
|
2001
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tom 46
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nr 1
7

Comprehensive analysis of all triple helical repeats in beta-spectrins reveals patterns of selective evolutionary conservation

84%
Baines A. J.
Cellular and Molecular Biology Letters
|
2003
|
tom 08
|
nr 1
The spectrin superfamily (spectrin, α-actinin, utrophin and dystrophin) has in common a triple helical repeating unit of ~106 amino acid residues. In spectrin, α and β chains contain multiple copies of this repeat. β-spectrin chains contain the majority of binding activities in spectrin and are essential for animal life. Canonical β-spectrins have 17 repeats; β-heavy spectrins have 30. Here, the repeats of five human β-spectrins, plus β-spectrins from several other vertebrates and invertebrates, have been analysed. Repeats 1, 2, 14 and 17 in canonical β are highly conserved between invertebrates and vertebrates, and repeat 8 in some isoforms. This is consistent with conservation of critical functions, since repeats 1, 2 and 17 bind α-spectrin. Repeats 1 of β-spectrins are not always detected by SMART or Pfam tools. A profile hidden Markov model of β-spectrin repeat 1 detects α-actinins, but not utrophin or dystrophin. Novel examples of repeat 1 were detected in the spectraplakins MACF1, BPAG1 and plectin close to the actin-binding domain. Ankyrin binds to the C-terminal portion of repeat 14; the high conservation of this entire repeat may point to additional, undiscovered ligand-binding activities. This analysis indicates that the basic triple helical repeat pattern was adapted early in the evolution of the spectrin superfamily to encompass essential binding activities, which characterise individual repeats in proteins extant today.
8

Protistan evolution and phylogeny: current controversies

84%
Kuznicki L., Walne P. L.
Acta Protozoologica
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1993
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tom 32
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nr 3
9

Phylogenetic studies of liverworts from the genus Pellia using a new type of a molecular marker

84%
Pacak A., Fiedorow P., Szweykowska-Kulinska Z.
Acta Societatis Botanicorum Poloniae
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2002
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tom 71
|
nr 3
10
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Pruning and grafting on the mammalian phylogenetic tree

84%
Archibald J. D.
Acta Palaeontologica Polonica
|
1999
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tom 44
|
nr 2
11

Genetic variation and molecular evolution of endangered Kozlov's pika (Ochotona koslowi Buchner) based on mitochondrial cytochrome b gene

67%
Lin G., Ci H., Thirgood S. J., Zhang T., Su J.
Polish Journal of Ecology
|
2010
|
tom 58
|
nr 3
Kozlov’s pika is a rare and endangered lagomorph species with a limited distribution in the southern Kunlun Mountains in western China. Because of its endangered status, Kozlov’s pika is considered a priority species for research and conservation action. Genetic variation and molecular evolution of the Kozlov’s pika were studied based on a total of 14 individuals from four locations along the eastern boundary between Xinjiang and Tibet province (35.20–36.48°N, 86.08–83.04°E) on extremely high elevation (usually over 4800 m a.s.l.). The density of local populations was about 3–4 per ha, living in a typical alpine desert grassland habitat. The complete mitochondrial cytochrome b (cytb) gene was amplified and sequenced. Based on the cytb gene sequences the genetic variation and molecular evolution were analyzed. Unexpected high haplotype diversity (0.956 ± 0.045) but low nucleotide diversity (0.00537 ± 0.00126) was found, indicating past demographic expansion. Significant partitioning of variance (P <0.01) among populations (46.7%), and within populations (53.3%), indicating low level of genetic differentiations among local populations. Our results gave an optimistic survival status of Kozlov’s pika at the genetic level. Bayes Empirical Bayes analysis with model M2a and M8 detected three positively selected amino acid sites at the significance level of 0.05. The mutant types with either or both of the mutations aspartic acid to asparagine and glutamic acid to lysine had higher isoelectric point values. We suggested these mutant types might have biological significance to help individuals to adapt to the extremely high elevation habitats.
12

Molecular evolution and acute phase change of guinea pig contrapsin and alpha-1-antiproteinase

67%
Suzuki Y., Sinohara H.
Folia Histochemica et Cytobiologica
|
1992
|
tom 30
|
nr 4
13

Molecular evolution and taxonomy of plants

67%
Zielinski R., Polok K.
Seria Biologiczna. Uniwersytet im. Adama Mickiewicza w Poznaniu
|
2005
|
tom 72
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