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Understanding the Role of a Thermophilic Genus Geobacillus in the Hydrolytic and Oxidative Degradation of Plant Biomass Insights from Genomics and Metagenomic Analyses
Published in Pratibha Dheeran, Sachin Kumar, Extremophiles, 2022
Tanvi Govil, David R. Salem, Rajesh K. Sani
Furthermore, there is a dearth of any comparative genomics on the mechanisms used by Geobacillus spp. to permit elaboration on how each species differ in the number of genes encoding for proteins and enzymes involved in attachment to lignocellulosic substrates. Like any other Gram-positive bacteria, the S-layer of Geobacillus comprises protein and carbohydrate polymers that helps them to maintain the required cell-substrate specificity. In one study, where Geobacillus stearothermophilus NRS 2004/3a served as model organism, WsaF, a rhamnosyltransferase, was proposed to function as both an enzyme and to promote adherence to a polysaccharide, a rhamnolipidin this case (Steiner et al. 2010). In the future, comparative genomics and proteomics studies aimed at identifying the proteins involved in attachment to cellulose, xylan, or any other plant biomass in their environment, and unique to various Geobacillus species, can provide important new insights into the ligninolytic capacity of this genus.
Using Molecular Methods to Identify and Monitor Xenobiotic-Degrading Genes for Bioremediation
Published in Ederio Dino Bidoia, Renato Nallin Montagnolli, Biodegradation, Pollutants and Bioremediation Principles, 2021
Edward Fuller, Victor Castro-Gutiérrez, Juan Carlos Cambronero-Heinrichs, Carlos E. Rodríguez-Rodríguez
Where multiple xenobiotic-degrading strains have been isolated, whole-genome sequencing and comparative genomics can be very powerful in the identification of novel genes. By identifying genes shared among three strains capable of mineralizing isoproturon, Yan et al. (2016) were able to narrow down the number of candidates to 84 gene sequences. From this number, manual curation was possible, and as such were able to identify and verify the isoproturon-mineralizing genes. This method has also been used to identify genes responsible for the degradation of other xenobiotic compounds, such as metaldehyde and chloroacetanilide (Cheng et al. 2019, Castro-Gutierrez et al. 2020). Since this strategy relies on similar degradative mechanisms and sequences to identify the novel gene(s), it is most powerful with a large dataset of degrading microorganisms. One drawback is that as xenobiotic compounds may be degraded using different degrading pathways in different microorganisms, degrading genes may not necessarily be identified using this approach.
Animal Biotechnology
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
C. elegans was the first multicellular organism to have its genome completely sequenced. The finished genome sequence was published in 1998, although a number of small gaps were present. The C. elegans genome sequence contains approximately 100 million bp and approximately 20,000 genes (Figure 7.5). The vast majority of these genes encode for proteins, but there are likely to be as many as 1000 RNA genes. Scientific curators continue to appraise the set of known genes such that new gene predictions continue to be added and incorrect ones modified or removed. In 2003, the genome sequence of the related nematode C. briggsae was also determined, allowing researchers to study the comparative genomics of these two organisms. Work is now ongoing to determine the genome sequences of more nematodes from the same genus such as C. remanei, C. japonica, and C. brenneri. These newer genome sequences are being determined by using the whole genome shotgun technique, which means that the resulting genome sequences are likely to not be as complete or accurate as that of C. elegans (which was sequenced using the “hierarchical” or clone-by-clone approach). The official version of the C. elegans genome sequence continues to change as and when new evidence reveals errors in the original sequencing, and we have to remember that DNA sequencing is not an error-free process.
Mercury methylation by anaerobic microorganisms: A review
Published in Critical Reviews in Environmental Science and Technology, 2019
Ming Ma, Hongxia Du, Dingyong Wang
As we mentioned above that biotic Hg methylation, namely MeHg formed by a series of anaerobic microorganisms, is the predominant driver of risk associated with Hg pollution. To date, anaerobic microorganisms involved in Hg methylation are found to be mainly sulfate-reducing bacteria (SRB) (Compeau & Bartha, 1985; Gilmour et al., 2011; Henry, 1992; Parks et al., 2013), iron-reducing bacteria (IRB) (Fleming, Mack, Green, & Nelson, 2006; Kerin et al., 2006), methanogens (Gilmour, Bullock, Mcburney, Podar, & Da, 2018; Hamelin, Amyot, Barkay, Wang, & Planas, 2011; Yu, Reinfelder, Hines, & Barkay, 2013), and other microorganisms such as fermentative, acetogenic, and cellulolytic microorganisms (Gilmour et al., 2013), all possessing a two-gene cluster hgcAB (Parks et al., 2013). The hgcAB genes are essential for Hg methylation, which is found by using comparative genomics and structural biology techniques (Parks et al., 2013). They renamed the DND132_1056 gene and its orthologs as hgcA, which was deduced to be a corrinoid-like protein during the formation of MeHg. The DND132_1057 gene and its orthologs were renamed as hgcB, which encoded a putative corrinoid-like protein linked to a 2[4Fe-4S] ferredoxin.
Which is most sensitive? Assessing responses of mice and rats in toxicity bioassays
Published in Journal of Toxicology and Environmental Health, Part A, 2018
Jessica Kratchman, Bing Wang, George Gray
The goal of toxicity testing is generally to assess human toxicity to chemicals and establish critical effects in the most sensitive gender and species to be used in chemical assessments and regulatory applications (U.S. Environmental Protection Agency 2016). Relative species or species-sex sensitivities might greatly influence regulatory toxicology determinations. Although there is not substantial literature describing why, the recommendation to assess all four species-sex groups such as male rats, female rats, male mice, and female mice this appears to be a convention adopted to ensure that the critical effect is captured. Discussions of relative sensitivities of animal subjects in the literature are generally considered within the context of a specific chemical or a specific health endpoint. In many cases, advances in basic biological knowledge including evolutionary biology, gene regulation and expression, comparative genomics, and pharmacokinetics facilitated more general understanding of species/sex differences and enables more nuanced application of bioassay data.
Identification and characterization of candidates involved in production of OMEGAs in microalgae: a gene mining and phylogenomic approach
Published in Preparative Biochemistry and Biotechnology, 2018
Vikas U. Kapase, Asha A. Nesamma, Pannaga P. Jutur
Due to their unique properties, microalgae represent an extremely diverse group of organisms, capable of converting atmospheric CO2 into promising feedstocks for applications in biofuels, nutraceuticals, functional foods, bioactive pharmaceuticals, and food and feed industries.[36] These eukaryotic algae are capable of producing poly unsaturated fatty acids (PUFAs), otherwise referred as OMEGA fatty acids (OMEGAs) namely eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).[37] These essential OMEGAs are known to be involved in regulation of mechanisms related to biological functions associated with cardiovascular disease and cancer prevention.[3] Exploration of metabolic pathways involved in the production of OMEGAs in microalgae is not yet exploited to full extent to engineer the pathways for enhanced production of these high-value added renewables. In the present study, our emphasis is prediction and characterization of proteins encoded by genes in the microalgal genomes through in silico approach involved in OMEGA biosynthetic pathway. Similar in silico studies involved in understanding of the global lipid biosynthetic pathway has demonstrated at the molecular level by comparative genomics and co-evolutionary analysis of metabolic pathways.[37–39] Henceforth, to characterize protein encoding genes of OMEGAs, comparative metabolic pathway analyses has been carried in eight different microalgal genomes, using defined combination dataset of homologous genes from reference models of A. thaliana and S. aggregatum, with a hypothesis of prediction of functional genes among microalgae. In this context, EC numbers, KEGG IDs, COGs, and GO terms were determined for all the respective candidate genes (Table 1).