Introduction

Lysyl tRNAs are essential for protein biosynthesis by ribosomal mRNA translation in all organisms. They are synthesized by Lysyl tRNA synthetases, a group of enzymes of two unrelated families; Class I tRNA synthetase and Class II tRNA synthetase. In bacteria and eukaryota, all known lysyl t-RNA synthetases are classified as Class II lysyl tRNA synthetases, whereas some archaea have been shown to contain an unrelated Class I-type lysyl tRNA synthetase. Recently, genomic analysis has revealed that the archaeal class I-type tRNA synthetase is detected in Treponema palladium and other spirochetes [Michael Ibba et al., 1997].

The understanding of taxonomical distribution in different organisms provides valuable information about gene transfer in various microbial pathogens. Interestingly, few microbial pathogens such as spirochetes were sequentially close relatives to Archaeal members. This is an evident based on computational analysis of Class I Lysyl t-RNA synthetase revealed that spirochetes may probably evolved from Archaeal kingdom. This computational analysis data would help researchers to understand in identifying common origin genes in different kingdoms and to discover organism specific molecular targets in pathogens which are taxonomical distributed only in bacteria and Archaea.[ Terada et al., 2002].

Material and Methods

Detection of subfamilies

Subfamily profile generation and comparison :

Results

BETE identified 3 subfamilies: Class I-type Lysyl tRNA synthetase_1, Class I-type Lysyl tRNA synthetase_2 and Class I-type Lysyl tRNA synthetase_3. The list of subfamilies and protein members present in microorganisms are summarized in table 1.

Figure 1

Table 1: The list of subfamilies of Class I-type Lysyl tRNA synthetase and Archaeal and bacterial members sharing different subfamilies.

Discussion

Bayesian Evolutionary Tree estimation (BETE) identified three functional subfamilies of a given Class I-type Lysyl tRNA synthetase multiple sequence alignment. Hidden markov models were useful in construction of subtypes of Class I-type Lysyl tRNA synthetase to search structural template in PDB database. The advantage of subfamily HMMs search against structural database and as well as sequential databases is to select suitable structural template for homology modeling of subfamily members which improves the quality of homology model. Moreover subfamily protein profiles are useful for homology searching and accurate protein family annotation at amino acid residue level which in turn helpful to recognize functionally and structurally important residues in different subfamilies. The family level comparison is not possible to determine exact functional annotation.

The Class I-type Lysyl tRNA synthetase are restricted to Archaeal and bacterial domains but not found in eukaryotes. Recent evidences showed that disease causing microorganisms such as Treponema palladium and Borrelia burgdorferi are orthologues to Archaeal members. The functional orthologous proteins in bacterial species and Archaeal species, not in Eukaryota, are the best drug protein targets.

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