Understanding Protein Function - The Disparity Between Bioinformatics and Molecular Methods

Abstract

Bioinformatics has its origins in the development of DNA sequencing methods by Alan Maxam and Walter Gilbert (Maxam and Gilbert, 1977), and by Frederick Sanger and coworkers (Sanger et al., 1977). By entirely different approaches, the first genomes determined at the nucleotide sequence level were that of bacteriophage φX174, and the recombinant plasmid named pBR322 composed of about 5,400 (Sanger et al., 1977), or 4,400 base pairs (Sutcliffe, 1979), respectively. In contrast, two articles that appeared in February 2001 reported on the preliminary DNA sequence of the human genome, which corresponds to 3 billion nucleotides of DNA sequence information (Lander et al., 2001; Venter et al., 2001). Only two years later, the GenBank sequence database contained more than 29.3 billion nucleotide bases in greater than 23 million sequences. With the development of new technologies, experts predict that the cost to sequence an individual’s DNA will be about $1000. This reduction in cost suggests that efforts in the area of comparative genomics will increase substantially, leading to an enormous database that vastly exceeds the existing one. By way of comparative genomics approaches, computational methods have led to the identification of homologous genes shared among species, and their classification into superfamilies based on amino acid sequence similarity. In combination with their evolutionary relatedness, superfamily members have been clustered into clades. In addition, high throughput sequencing of small RNAs and bioinformatics analyses have contributed to the identification of regions between genes that can code small RNAs (siRNA, microRNA, and long noncoding RNA), which act during the development of an organism to modulate gene expression at the post-transcriptional level (Fire et al., 1998; Hamilton and Baulcombe, 1999) reviewed in Elbashir et al., 2001; Ghildiyal and Zamore, 2009; Christensen et al., 2010). An emerging area is functional genomics whereby gene function is deduced using largescale methods by identifying the involvement of specific genes in metabolic pathways. More recently, phenotype microarray methods have been used to correlate the functions of genes of microbes with cell phenotypes under a variety of growth conditions (Bochner, 2009). These methods contrast with the traditional approach of mapping a gene via the phenotype of a mutation, and deducing the function of the gene product based on its biochemical analysis in concert with physiological studies. Such studies have been performed to confirm the functional importance of conserved residues shared by superfamily members, and also