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Molecular Biology and Bioinformatics in Industrial Microbiology and Biotechnology
Published in Nduka Okafor, Benedict C. Okeke, Modern Industrial Microbiology and Biotechnology, 2017
Nduka Okafor, Benedict C. Okeke
After the identification of gene-functions, a natural step is to perform pair-wise genome comparisons. Pair-wise genome comparison of a genome against itself provides the details of paralogous genes (duplicated genes that have similar sequence with some variation in function). Pair-wise genome comparisons of a genome against other genomes have been used to identify a wealth of information such as orthologous genes (functionally equivalent genes diverged in two genomes due to speciation), different types of gene-groups (adjacent genes that are constrained to occur in close proximity due to their involvement in some common higher level function), lateral gene-transfer (gene transfer from a microorganism that is evolutionary distant), gene-fusion/gene-fission, gene-group duplication, gene- duplication, and difference analysis to identify genes specific to a group of genomes such as pathogens, and conserved genes.
The enigma of environmental organoarsenicals: Insights and implications
Published in Critical Reviews in Environmental Science and Technology, 2022
Xi-Mei Xue, Chan Xiong, Masafumi Yoshinaga, Barry Rosen, Yong-Guan Zhu
The most thoroughly characterized mechanisms for arsenical biotransformation are arsenic methylation and demethylation. In 2006, ArsM from the soil bacterium Rhodopseudomonas palustris was characterized both in vivo and in vitro using heterologous expression in Escherichia coli and purified protein to catalyze sequential methylation of As(III), producing mono-, di- and tri-methylated species with tri-methylarsine gas as the end product (Fig. 1A) (Qin et al., 2006). ArsM orthologs have been identified in eukaryotes, including metazoan, fungi, and algae, where arsM genes were acquired horizontal gene transfer between different kingdoms of life (Chen et al., 2017). AS3MT from humans and mice are ArsM orthologs involved in arsenic methylation. Crystal structures of CmArsM, the ArsM ortholog from the thermophilic eukaryotic red alga Cyanidioschyzon merolae, were solved with no ligands (Ajees et al., 2012), with bound S-adenosylmethionine (SAM) (Ajees et al., 2012), As(III) (Ajees et al., 2012), MAs(III) (Packianathan et al., 2018a), phenylarsenite (Packianathan et al., 2018a), trivalent roxarsone (Packianathan et al., 2018a), or with both S-adenosylhomocysteine and As(III) (Packianathan et al., 2018b). Based on function-structure analyses with these solved crystal structures, a disulfide-bond cascade mechanism model has been proposed for the mechanism of ArsM (Marapakala et al., 2015), which explains how the product is maintained in the trivalent state during the catalytic cycle.
Potency matters: Impacts of embryonic exposure to nAChR agonists thiamethoxam and nicotine on hatching success, growth, and neurobehavior in larval zebrafish
Published in Journal of Toxicology and Environmental Health, Part A, 2022
Shayla Victoria, Megan Hein, Elisabeth Harrahy, Tisha C King-Heiden
It should be noted that the H. sapiens protein sequence was used as a vertebrate model due to the lack of zebrafish nAChR protein structure, with the assumption that there is sequence homology in the nAChR binding site across most vertebrate organisms, as most studies using zebrafish as a model system do. However, a BLAST sequence alignment of D. rerio nAChR subunits (alpha-3 ligand binding domain and alpha subunit) with their H. sapiens orthologs revealed that the D. rerio sequences are 84.4% and 75.4% similar to the H. sapiens sequences, respectively, with similar homology to other mammals (rat and mouse). As expected, the nAChR subunit sequences in D. rerio were similar to orthologs in other fish species, including C. auratus (97.6% and 97.1%) and T. tibetana (97.1% and 93.7%). The sequence similarity of D. rerio nAChR proteins to mammals suggests that fish need to be protected from marked overt toxic responses from TM exposure, as observed in the present study. However, since adverse effects following exposure to sublethal concentrations of TM were noted in D. rerio and in other larval fishes, additional studies need to be conducted to further examine the potential risks that neonicotinoid pesticides pose to non-target species. Our data also demonstrate that molecular dynamics (MD) simulations might be useful for gaining a better understanding of the dynamic protein–ligand interactions that underly observed toxic responses by enabling some realistic flexibility in the binding site. In addition, using a fish nAChR protein structure in modeling software might be ideal to more accurately relate the observed physiological and behavioral alterations to protein–ligand interactions.