Representation of a tree with p hanging vertices by 2p?3 elements of its distance matrix

Yushmanov, S. V.

doi:10.1007/bf01139951

Cited by 9 publications

(16 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…(B) Phylogenetic tree of the mature MGDG synthases. The tree was built using the cluster algorithm developed by Chumakov and Yushmanov [26], with MGDG synthase sequences shortened from their transit peptides.…”

Section: Resultsmentioning

confidence: 99%

“…1) is not only due to the presence of a transit peptide. Figure 1B shows a phylogenetic tree built with the cluster algorithm developed by Chumakov and Yushmanov [26], using MGDG synthases sequences, shortened from their putative transit peptides. Clearly, mature proteins of MGD A, MGD B and MGD C belong to two diverging groups within the MGDG synthase family of proteins.…”

Section: Resultsmentioning

confidence: 99%

“…1). Mature protein sequences from classes A, B and C (without transit peptides) also belong to diverging homology groups, as determined from distance matrices upon the cluster algorithm developed by Yushmanov ([26]; Fig. 1B).…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Biochemical and topological properties of type A MGDG synthase, a spinach chloroplast envelope enzyme catalyzing the synthesis of both prokaryotic and eukaryotic MGDG

Miège

Maréchal

Shimojima

et al. 1999

European Journal of Biochemistry

119

110

View full text Add to dashboard Cite

MGDG synthase, the enzyme that catalyzes the synthesis of the major chloroplast membrane lipid monogalactosyldiacylglycerol (MGDG), is encoded by a multigenic family. We have analyzed the biochemical properties, subcellular localization and membrane topology of a spinach chloroplast MGDG synthase, a representative member of the type A family from Spinacia oleracea (soMGD A), using a recombinant protein that was functionally overexpressed in Escherichia coli and specific polyclonal antibodies. We demonstrated that soMGD A could catalyze the synthesis of both`prokaryotic' and`eukaryotic' MGDG molecular species in vitro, with a selectivity for diacylglycerol similar to that of purified chloroplast envelope MGDG synthase activity. Furthermore, soMGD A was shown to be sensitive to chemical reagents (dithiothreitol, N-ethylmaleimide and o-phenanthroline) known to affect MGDG synthesis by the partially purified enzyme, as well as in isolated chloroplast envelope membranes. In spinach chloroplasts, soMGD A was localized by Western blot analysis in the inner envelope membrane. Topological studies demonstrated that soMGD A is a monotopic enzyme, embedded within one leaflet of the inner envelope membrane from spinach chloroplasts, a structure which may involve amphipathic a helices. We further demonstrated that in vitro, soMGD A precursor is imported and processed to its correct mature form in intact chloroplasts. These results show that soMGD A corresponds to a mature polypeptide of < 45 kDa. In addition, inactivation kinetics after g-ray irradiation strongly suggest that both native chloroplast envelope MGDG synthase and recombinant soMGD A have a functional molecular mass of 95±100 kDa, indicating that they are probably active as homodimers made of two 45-kDa subunits. This study suggests that, in spite of the growing evidence that MGDG synthesis is catalyzed by a multigenic family of enzymes, in spinach leaves both prokaryotic and eukaryotic MGDG syntheses could be attributable to a unique dimeric enzyme, provided that diacylglycerol is transported from the outer membrane to the inner membrane of the chloroplast envelope.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Biochemical and topological properties of type A MGDG synthase, a spinach chloroplast envelope enzyme catalyzing the synthesis of both prokaryotic and eukaryotic MGDG

Miège

Maréchal

Shimojima

et al. 1999

European Journal of Biochemistry

119

110

View full text Add to dashboard Cite

show abstract

“…In general this appears a difficult question (indeed determining whether such a partial d-metric is realized by any tree is NP-hard [5]). However, some sufficient conditions (as well as some necessary conditions) for uniqueness to hold have been found, in [3,12], and more recently in [4], and [7]. In this paper we consider the uniqueness question for trees that are 'fully-resolved' (i.e.…”

Section: Introductionmentioning

confidence: 99%

Tree Reconstruction from Triplet Cover Distances

Huber

Steel

2014

Electron. J. Combin.

View full text Add to dashboard Cite

It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict subset L of leaf pairs to suffice for reconstructing the tree and its edge weights, given just the distances between the leaf pairs in L. It is known that any set L with this property for a tree in which all interior vertices have degree 3 must form a cover for T -that is, for each interior vertex v of T , L must contain a pair of leaves from each pair of the three components of T − v. Here we provide a partial converse of this result by showing that if a set L of leaf pairs forms a cover of a certain type for such a tree T then T and its edge weights can be uniquely determined from the distances between the pairs of leaves in L. Moreover, there is a polynomial-time algorithm for achieving this reconstruction. The result establishes a special case of a recent question concerning 'triplet covers', and is relevant to a problem arising in evolutionary genomics.

show abstract

“…A circular order has the property that for any integer k (modulo n ) all the branches on the path P ( x k , x k+ 1 ) between x k and x k+ 1 correspond to the left branch (or right branch if anti-clockwise). Makarenkov and Leclerc (1997, 2000) have shown that the concept of circular ordering is equivalent to the so-called Yushmanov’s ordering (Yushmanov, 1984). A simple ordering algorithm can be used to order the leaves.…”

Section: Circular Ordering = Ordering Of a Transformed Distance Matrixmentioning

confidence: 99%

Minimizing Contradictions on Circular Order of Phylogenic Trees

Thuillard¹

2007

Evol Bioinform Online

View full text Add to dashboard Cite

Distance-based approaches to phylogeny use estimations of the evolutionary distance between sequences to reconstruct an evolution tree. If the evolution can be represented by an X-tree, the different sequences can be ordered so that the distance matrix , n i j Y , representing the distance from a leaf n to the path (i, j ), is perfectly ordered meaning that ,After ordering of the sequences, the distance matrix Y i j n , permits to visualize phylogenetic relationships between taxa and to localize deviations from perfect order. The effect of perturbations resulting from lateral gene transfer or crossover can be modeled probabilistically. The order is shown to be quite robust against many perturbations. We have developed algorithms to minimize the level of contradiction in the order of the sequences. These algorithms are tested on the SSU rRNA data for Archaea. The degree of contradiction after optimization is for most taxa quite low. Regions in the taxa space with deviations from perfect order were identifi ed.

show abstract

Representation of a tree with p hanging vertices by 2p?3 elements of its distance matrix

Cited by 9 publications

References 3 publications

Biochemical and topological properties of type A MGDG synthase, a spinach chloroplast envelope enzyme catalyzing the synthesis of both prokaryotic and eukaryotic MGDG

Biochemical and topological properties of type A MGDG synthase, a spinach chloroplast envelope enzyme catalyzing the synthesis of both prokaryotic and eukaryotic MGDG

Tree Reconstruction from Triplet Cover Distances

Minimizing Contradictions on Circular Order of Phylogenic Trees

Contact Info

Product

Resources

About