Alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout its biology, consisting of catalytic, tRNA-recognition, editing, and C-Ala domains. The catalytic and tRNA-recognition domains catalyze aminoacylation, the editing domain hydrolyzes mischarged tRNAAla, and C-Ala―the major tRNA-binding module―targets the elbow of the L-shaped tRNAAla. Interestingly, a mini-AlaRS lacking the editing and C-Ala domains is recovered from the Tupanvirus of the amoeba Acanthamoeba castellanii. Here we show that Tupanvirus AlaRS (TuAlaRS) is phylogenetically related to its host’s AlaRS. Despite lacking the conserved amino acid residues responsible for recognition of the identity element of tRNAAla (G3:U70), TuAlaRS still specifically recognized G3:U70-containing tRNAAla. In addition, despite lacking C-Ala, TuAlaRS robustly binds and charges microAla (an RNA substrate corresponding to the acceptor stem of tRNAAla) as well as tRNAAla, indicating that TuAlaRS exclusively targets the acceptor stem. Moreover, this mini-AlaRS could functionally substitute for yeast AlaRS in vivo. This study suggests that TuAlaRS has developed a new tRNA-binding mode to compensate for the loss of C-Ala.

Unlike many other aminoacyl-tRNA synthetases, alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout biology. While Caenorhabditis elegans cytoplasmic AlaRS (CeAlaRSc) retains the prototype structure, its mitochondrial counterpart (CeAlaRSm) contains only a residual C-terminal domain (C-Ala). We demonstrated herein that the C-Ala domain from CeAlaRSc robustly binds both tRNA and DNA. It bound different tRNAs but preferred tRNAAla. Deletion of this domain from CeAlaRSc sharply reduced its aminoacylation activity, while fusion of this domain to CeAlaRSm selectively and distinctly enhanced its aminoacylation activity toward the elbow-containing (or L-shaped) tRNAAla. Phylogenetic analysis showed that CeAlaRSm once possessed the C-Ala domain but later lost most of it during evolution, perhaps in response to the deletion of the T-arm (part of the elbow) from its cognate tRNA. This study underscores the evolutionary gain of C-Ala for docking AlaRS to the L-shaped tRNAAla.

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The separation of Sumatra and Java occurred at the end of the Miocene (10 mya) to the end of Pliocene (1.8 mya). The existence of ecological variations and geographic barriers inhibits gene flow through the isolation of adaptation, geography, reproduction, inbreeding, and leading to population segregation. Cobra (genus Naja) distribution became greatly influenced by the geologic condition and sea level. This study was conducted by phylogenetic analysis towards the 16S rRNA gene. Survey was done with Visual Encounter Survey (VES) method on 6 locality. There were 3 location in Sumatra Island and the others in Java Island. Sample from other Asian region was obtained from Genbank, which are 11 individuals from China, Thailand, and Nepal. DNA extraction was done according to the QIAmp ® DNA Mini Kit standard protocol. The forward and reverse 16S sequences are combined with the Sequencher TM version 4.1.4 program, then in BLAST (Blast Local Alignment Search Tool) at www.ncbi.nlm.nih.gov. Phylogenetic analyzes of clade A (MP = 60, ML = 54, BI = 88) indicate the presence of division into two monophyletic subclade (AI and AII). Subclade AI consists of groups of Cobra from Sunda (Thailand, Sumatra and Java). Subclade AII is a group of species N. kaouthia originating from Chumpon Province, Southern Thailand with (MP = 96, ML = 95, BI = 100). Clade B is divided into two subclasses (BI and BII). The result is supported by bootstrap value MP = 93, ML = 99, BI = 100. N. atra of Fujian Province is a sister lineage of the same species from Jiangxi Province (MP = 86, ML = 86, BI = 100).