Comparative protein analysis of the chitin metabolic pathway in extant organisms: a complex network approach.
Chitin is a structural endogenous carbohydrate, which is a major component of fungal cell walls and arthropod exoskeletons. A renewable resource and the second most abundant polysaccharide in nature after cellulose, chitin is currently used for waste water clearing, cosmetics, medical, and veterinary applications. This work comprises data mining of protein sequences related to the chitin metabolic pathway of completely sequenced genomes of extant organisms pertaining to the three life domains, followed by meta-analysis using traditional sequence similarity comparison and complex network approaches. Complex networks involving proteins of the chitin metabolic pathway in extant organisms were constructed based on protein sequence similarity. Several usual network indices were estimated in order to obtain information on the topology of these networks, including those related to higher order neighborhood properties. Due to the assumed evolutionary character of the system, we also discuss issues related to modularity properties, with the concept of edge betweenness playing a particularly important role in our analysis. Complex network approach correctly identifies clusters of organisms that belong to phylogenetic groups without any a priori knowledge about the biological features of the investigated protein sequences. We envisage the prospect of using such a complex network approach as a high-throughput phylogenetic method.
Góes-Neto
Aristóteles
A
Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia 44036-900, Brazil. arigoesneto@pq.cnpq.br
Diniz
Marcelo V C
MV
Santos
Leonardo B L
LB
Pinho
Suani T R
ST
Miranda
José G V
JG
Lobao
Thierry Petit
TP
Borges
Ernesto P
EP
El-Hani
Charbel Niño
CN
Andrade
Roberto F S
RF
D000595:Amino Acid Sequence; D001105:Archaea / Q000378:metabolism*; D001419:Bacteria / Q000378:metabolism*; D002686:Chitin / Q000378:metabolism*; D003198:Computer Simulation; D056890:Eukaryota / Q000378:metabolism*; D008954:Models, Biological; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction / Q000502:physiology*; D013045:Species Specificity
D011506:Proteins; D002686:Chitin