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Microbial Biotechnology
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
Transposable genetic elements are segments of DNA that have the capacity to move from one location to another (i.e., jumping genes). Transposable genetic elements can move from any DNA molecule to any DNA of another molecule, or even to another location on the same molecule. The movement is not totally random. There are preferred sites in a DNA molecule at which the transposable genetic element will insert. The transposable genetic elements do not exist autonomously; thus, to be replicated, they must be a part of some other replicon. Transposition requires little or no homology between the current location and the new site. The transposition event is mediated by an enzyme, transposase, which is coded by the transposable genetic element. Recombination that does not require homology between the recombining molecules is called illegitimate or nonhomologous recombination. In many instances, transposition of the transposable genetic element results in the removal of the element from the original site and insertion at a new site. However, in some cases, the transposition event is accompanied by the duplication of the transposable genetic element. One copy remains at the original site and the other is transposed to the new site.
Microbial biotechnology
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2018
Transposable genetic elements are segments of DNA that have the capacity to move from one location to another (i.e., jumping genes). Transposable genetic elements can move from any DNA molecule to any DNA of another molecule, or even to another location on the same molecule. The movement is not totally random. There are preferred sites in a DNA molecule at which the transposable genetic element will insert. The transposable genetic elements do not exist autonomously; thus, to be replicated, they must be a part of some other replicon. Transposition requires little or no homology between the current location and the new site. The transposition event is mediated by an enzyme, transposase, which is coded by the transposable genetic element. Recombination that does not require homology between the recombining molecules is called illegitimate or nonhomologous recombination. In many instances, transposition of the transposable genetic element results in the removal of the element from the original site and insertion at a new site. However, in some cases, the transposition event is accompanied by the duplication of the transposable genetic element. One copy remains at the original site and the other is transposed to the new site.
Human-Induced Pluripotent Stem Cells: Derivation
Published in Deepak A. Lamba, Patient-Specific Stem Cells, 2017
Uthra Rajamani, Lindsay Lenaeus, Loren Ornelas, Dhruv Sareen
PiggyBac transposon—PiggyBac transposons allow for the efficient delivery of reprogramming factors by means of a cut–paste mechanism. A transposase can integrate to the chromosomal TTAA site that can later be excised from the genome upon reexpression of transposase. This system has been shown to be efficient in excisable gene delivery of up to 10 kb DNA fragments (100). The PiggyBac transposon system can be completely removed from the host genome without changing sequences at the integration sites (101). The PiggyBac reprogramming technique thus allowed the generation of mouse and human iPSCs by using tetracycline-inducible or polycistronic expression of reprogramming factors (102–104). This method reported a high efficiency rate of 2.5%. This system provides an efficient nonintegrative reprogramming approach with minimal changes to host genome. However, transposase excision of transgenes could still be accompanied by microdeletions of genomic DNA (101), which questions its clinical applications. Also, a small footprint of the plasmid may be left behind.
High-throughput profiling the effects of zinc on antibiotic resistance genes in the anaerobic digestion of swine manure
Published in Environmental Technology, 2023
Ranran Zhang, Chenpan Gong, Menglong Liu, Liuyuan Zhou, Haifeng Zhuang, Zhijun Hu
Overall, 118, 119, and 119 unique ARGs were detected in CK, ZnL, and ZnH, respectively. Thus, the numbers of ARGs did not differ greatly among the three treatments (Figure 1(a)). Multidrug and aminoglycoside ARGs were most frequent and they accounted for 24–25% of those detected in all treatments, followed by MLSB (accounted for 17–18%) and tetracycline (accounted for 8%) ARGs. In addition, beta-lactam and trimethoprim ARGs accounted for 6–8%, and phenicol and fluoroquinolone ARGs accounted for 3–4% in the three treatments. Most of these ARGs were found in all three treatments. However, a small number of subtypes were found in the zinc treatments (Table S2). In particular, aac(3)-xa, vanHB, erm(36), mphA, mexB, arr-2, apmA, oqxA, tcrB, and dfrG were not found in CK, but they were detected in ZnL or ZnH. Some subtypes were also not detected in the zinc treatments, but they were present under CK, such as vanB and ceoA. Moreover, 28, 30, and 28 unique MGEs were detected in CK, ZnL, and ZnH, respectively (Figure 1(c)). Most of the MGEs were found in all three treatments, with a few exceptions. In particular, intl3 (integrase) and IS21-ISAs29 (transposase) were present under CK but not in the zinc treatments. Some transposases (IS256, IS91, and ISCR1) were not detected under CK but they were present in the two zinc treatments (Table S2).
Effect of multiple heavy metals pollution to bacterial diversity and community structure in farmland soils
Published in Human and Ecological Risk Assessment: An International Journal, 2021
Chuanzhang Li, Xiaofei Wang, He Huang, Lin Wang, Feng Wei, Chaolan Zhang, Qun Rong
Bacteria adapts to high heavy metal pollution by changing their community abundance and structure (Liao et al. 2010; Deng et al. 2015). At the phylum level, Proteobacteria, Chloroflexi, Acidobacteria and Actinobacteria were dominant in all the samples. Previous studies show that Proteobacteria, Chloroflexi, Acidobacteria and Actinobacteria are the normal phyla in soil (Yin et al. 2019). However, there were differences in relative abundance, with each level having its own unique bacterial populations. HR samples exhibited a higher relative abundance in Acidobacteria, which was considered the core resistance phyla in HR soils. Further, some members of Acidobacteria resistant to acidic pH and heavy metals such as norank_f__Acidobacteriaceae__Subgroup_1_, Candidatus_Solibacter (Ying et al. 2014; Gołębiewski et al. 2014). Similarly, the abundance of Gemmatimonadetes increased with pollution level, which has previously been reported to survive in heavy metal polluted soils (Lur et al. 2015). Chloroflexi had the similar relative abundance in MR (23.17%) and HR (22.71%), while the lowest relative abundance was in LR (14.07%). Many species of Chloroflexi are slow-growing, versatile and facultatively aerobic photoheterotrophs, have been previously reported to be resistant to heavy metals (Lur et al. 2015; Azarbad et al. 2015). Just like Ktedonobacteria, as one clade of the phylum Chloroflexi, was significantly enriched in HR samples. Ktedonobacteria has an unusually large transposases, implicated in high metabolic plasticity (Chang et al. 2011). The presence of several highly expressed transcripts with putative transposase or integrase activity enables Ktedonobacteria to adapt to high levels of pollution (Lur et al. 2015). Contrary to our findings, previous studies showed that high abundances of Proteobacteria, Actinobacteria and Bacteroidetes in heavy metal-polluted samples (Azarbad et al. 2015; Chen et al. 2018). In our study, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant bacteria in LR samples. This difference can be attributed to the high pH of LR samples. Soil pH was a key environmental factor for bacteria, which can strongly impact relative abundances of certain groups of bacteria in soils (Shen et al. 2013; Wang et al. 2018). Our findings show that low pH enriches Acidobacteria while the abundances of Proteobacteria, Actinobacteria and Bacteroidetes increased with pH (Mã¤nnistö et al. 2007; Lauber et al. 2009).