A use for principal Coordinate analysis in the comparison of protein sequences

Woolley, Kevin J.; Athalye, M.

doi:10.1016/0006-291x(86)90705-9

Cited by 5 publications

(7 citation statements)

References 9 publications

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“…Introduced in the field of sequence analysis more than 20 years ago [26], mutidimensional scaling analysis was applied to the analysis of protein families [26], [27], [28], [29], [30], of the protein fold space [31], [32], [33], of virus evolution [34], [35], [36], [37] and of large genomic data sets [38]. This method usefully complements phylogenetic techniques and provides important insights into the evolution of proteins, genes and virus.…”

Section: Discussionmentioning

confidence: 99%

Multidimensional Scaling Reveals the Main Evolutionary Pathways of Class A G-Protein-Coupled Receptors

et al. 2011

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Class A G-protein-coupled receptors (GPCRs) constitute the largest family of transmembrane receptors in the human genome. Understanding the mechanisms which drove the evolution of such a large family would help understand the specificity of each GPCR sub-family with applications to drug design. To gain evolutionary information on class A GPCRs, we explored their sequence space by metric multidimensional scaling analysis (MDS). Three-dimensional mapping of human sequences shows a non-uniform distribution of GPCRs, organized in clusters that lay along four privileged directions. To interpret these directions, we projected supplementary sequences from different species onto the human space used as a reference. With this technique, we can easily monitor the evolutionary drift of several GPCR sub-families from cnidarians to humans. Results support a model of radiative evolution of class A GPCRs from a central node formed by peptide receptors. The privileged directions obtained from the MDS analysis are interpretable in terms of three main evolutionary pathways related to specific sequence determinants. The first pathway was initiated by a deletion in transmembrane helix 2 (TM2) and led to three sub-families by divergent evolution. The second pathway corresponds to the differentiation of the amine receptors. The third pathway corresponds to parallel evolution of several sub-families in relation with a covarion process involving proline residues in TM2 and TM5. As exemplified with GPCRs, the MDS projection technique is an important tool to compare orthologous sequence sets and to help decipher the mutational events that drove the evolution of protein families.

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Section: Discussionmentioning

confidence: 99%

Multidimensional Scaling Reveals the Main Evolutionary Pathways of Class A G-Protein-Coupled Receptors

et al. 2011

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“…The phylogenetic tree of fungal cellulases belonging to family 7 of the glycosyl hydrolases including the three I. lacteus cellulases, Cel1, Cel2, and Cel3 encoded by different three genes ( cel1, cel2 , and cel3 ) was constructed using the unweighted pair‐group method with arithmetic mean (UPGMA) method [13]. The phylogenetic tree (Fig.…”

Section: Resultsmentioning

confidence: 99%

Cloning and characterization of a new exo-cellulase gene,cel3, inIrpex lacteus

Hamada

Fuse

Shimosaka

et al. 1999

FEMS Microbiology Letters

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A new cellulose-inducible gene (named cel3) was isolated from a strain of the white rot basidiomycete, Irpex lacteus MC-2. The cel3 open reading frame, containing two introns, encodes a polypeptide of 526 amino acids residues with a molecular mass of 55794 Da. Expression of the cel3 gene was induced by various insoluble celluloses and CM-cellulose. Transcription of cel3 was abolished when cells were cultivated in media containing the above cellulosic substrates, but added with glucose, fructose or lactose, while addition of glycerol or mannitol did not affect the cel3 mRNA level. The amino acid sequence of the catalytic domain of the Cel3 protein was homologous to that of fungal exo-type cellulases belonging to family 7 of the glycosyl hydrolases. A phylogenetic study showed that these exo-type cellulases can be clearly separated from family 7 endo-type cellulases.

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“…MDS, also named principal coordinate analysis, starts from a matrix of distances between elements and visualizes these elements in a low dimensional space in which the distances best approximate the original distances. Applied to biological sequences, this method usefully complements phylogeny [6-11]. …”

Section: Introductionmentioning

confidence: 99%

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling

et al. 2012

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BackgroundThe distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to protein families, MDS provides information complementary to the information derived from tree-based methods. Moreover, MDS gives a unique opportunity to compare orthologous sequence sets because it can add supplementary elements to a reference space.ResultsThe R package bios2mds (from BIOlogical Sequences to MultiDimensional Scaling) has been designed to analyze multiple sequence alignments by MDS. Bios2mds starts with a sequence alignment, builds a matrix of distances between the aligned sequences, and represents this matrix by MDS to visualize a sequence space. This package also offers the possibility of performing K-means clustering in the MDS derived sequence space. Most importantly, bios2mds includes a function that projects supplementary elements (a.k.a. “out of sample” elements) onto the space defined by reference or “active” elements. Orthologous sequence sets can thus be compared in a straightforward way. The data analysis and visualization tools have been specifically designed for an easy monitoring of the evolutionary drift of protein sub-families.ConclusionsThe bios2mds package provides the tools for a complete integrated pipeline aimed at the MDS analysis of multiple sets of orthologous sequences in the R statistical environment. In addition, as the analysis can be carried out from user provided matrices, the projection function can be widely used on any kind of data.

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A use for principal Coordinate analysis in the comparison of protein sequences

Cited by 5 publications

References 9 publications

Multidimensional Scaling Reveals the Main Evolutionary Pathways of Class A G-Protein-Coupled Receptors

Multidimensional Scaling Reveals the Main Evolutionary Pathways of Class A G-Protein-Coupled Receptors

Cloning and characterization of a new exo-cellulase gene,cel3, inIrpex lacteus

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling

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