IOSR Journal of Agriculture and Veterinary Science (IOSR-JAVS) e-ISSN: 2319-2380, p-ISSN: 2319-2372. Volume 9, Issue 2 Ver. I (Feb. 2016), PP 24-30 www.iosrjournals.org DOI: 10.9790/2380-09212430 www.iosrjournals.org 24 | Page Sequencing and Translational Analysis Revealed Huge Mutation in the N-Terminus End of Leader Proteinase (Lpro) Gene of Foot and Mouth Disease Viruses Isolated From Cattle in Bangladesh Islam MS, Ruba T, Habib MA, Rima UK, Hossain MZ, Saha PC, Das PM And *Khan MAHNA Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh. Abstract: Foot and Mouth Disease virus (FMDV) comprises four structural and ten nonstructural proteins in its genome. The Leader proteinase (Lpro) is structurally and functionally related to papain-like cysteine proteinase with catalytic cystein and histidine residues which is the first functional component of the Aphthoviral polyprotein. Complete Lpro genes of six Bangladeshi isolates of FMDV of three different serotypes were sequenced and compared with each other as well as with those sequences available in the GenBank to evaluate the extent of mutation in this gene. Out of six isolates investigated a serotype O viruses (BD_SI_5_2013) showed highest level of amino acid (aa) substitution with a critical substitution at L 10 by V 10 . The Lpro gene of the investigated viruses showed mutation in 9% (≤) nucleotide and substitution of aa in 11.4% position. A total of 55% variability of aa was seen in the N terminus end between first two conserved initiation codons at 1 st and 29 th aa positions of Lpro sequences. Methionine at position 1, 29, 126 and 132 are conserved in the Lpro sequences. The L ab form of the Lpro was found more variable than L b form. Conserved KRLK/R sequence was found at Lpro/VP4 cleavage site at the C terminus end of Lpro in all the isolates. The invariant motif, the catalytic triad and other critical amino acids were totally conserved. Specific clustering of viruses on the basis of serotype as well as geographical origin was not found in the phylogenetic trees constructed but the viruses had lineage specific signature clustered together in Maximum Likelihood (ML) tree. Keywords: Clustering, FMDV, Lpro gene, Sequencing, Substitution of amino acid I. Introduction FMD is a highly contagious viral disease of cloven hoofed ruminants caused by FMD virus (FMDV) showing symptoms like fever, formation of vesicles on the mouth, tongue, interdigital spaces and teats (Shanmugam et al., 2015, APHIS, 2007). The disease is endemic in Bangladesh and frequently confer epidemic tremor with a gap of few years. Annual losses due to FMD in Bangladesh were estimated at about US$62 million (FAO/OIE, 2012). Direct loss in lactating animals is 15% of the total yield. Moreover, the disease is a cause of infertility, abortion, calf mortality and reduced efficiency of work animals. Affected animals hardly attain their original production potential (Rubina et al., 2002). The etiological agent is a single stranded RNA virus of the Aphthovirus genus, family Picornaviridae, occurring in seven serotypes (O, A, C, Asia-1, SAT1, SAT2, and SAT3) and more than 65 subtypes (Saiz et al., 2002; Brown, 2003). FMDV consists of a single- stranded, plus sense RNA genome of approximately 8,500 bases surrounded by four structural proteins that form an icosahedral capsid. The genome contains 5′ UTR (untranslated region), 3′UTR and a long open reading frame (ORF) which can be translated into a single polyprotein, that can be cleaved into four (VP4, VP2, VP3 and VP1) structural proteins and 10 (L, 2A, 2B, 2C, 3A, 3B1, 3B2, 3B3, 3C, and 3D) non-structural proteins (Feng, 2004). The Leader proteinase (Lpro) is a structurally and functionally related papain-like cysteine proteinase gene with catalytic cystein and histidine residues which is the first functional component of the FMDV polyprotein that plays a significant role in the cleavage of the viral polyprotein at the L/P1 junction. In the cleavage of host protein initiation factors e1F-4F Lpro involved in translation of capped mRNAs, and evasion of the host innate immune response (Shanmugam et al., 2015; Piccone et al., 2011; Piccone et al., 2010; Guarne et al., 2000; Medina et al., 1993; Strebel and Beck, 1986). The Lpro gene is situated at the extreme 5′ end of the coding region of FMDV RNA that contains the first functional initiation codon (AUG) for the whole ORF at position 01. Another AUG codon is present at 84 bases apart in the same ORF (Sanger et al., 1987; Belsham 1992).The N terminus end of the Lpro sequences showed increased amino acid variations with 2 conserved start codons at 1 st and 29 th site. Lpro gene showed its high variability in the nucleotide sequences as comparable to that of the structural proteins (George et al., 2001; Carrillo et al., 2005). Among the sequences of two forms of Lpro, the L ab showed a high variability than the L b form. All the critical amino acid residues of the active cleft site are conserved. The phylogenetic analysis of the Lpro region sequences showed a difference in clustering of isolates as observed with the VP1 capsid coding region sequencing. Thus, the Lpro region phylogeny could be