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Classifications and typical examples of biomotors
Published in Peixuan Guo, Zhengyi Zhao, Biomotors: Linear, Rotation, and Revolution Motion Mechanisms, 2017
Nucleocytoplasmic large DNA viruses (NCLDV) superfamily include viruses such as Mimivirus, Megavirus, Pandoravirus and Pithovirus (La et al., 2003; Arslan et al., 2011; Philippe et al., 2013) and infect a wide range of eukaryotes (Ghedin and Fraser, 2005; Chelikani et al., 2014b). These viruses are also called giant viruses due to their sheer size (larger than some bacteria). Typical example of these viruses is Mimiviruses which package their 1.2 Mbp dsDNA genome into preformed procapsids through a nonvertex portal (Zauberman et al., 2008) driven by the vaccinia virus A32-type virion packaging ATPase (Monier et al., 2008). It has been shown that the structure and function of their DNA packaging motors are homologous to the FtsK DNA translocase (Iyer et al., 2004; Chelikani et al., 2014b) and use similar revolving mechanism for genome packaging (Iyer et al., 2004; Guo et al., 2016). The genome packaging motors of NCLDVs interact with other genome packaging components such as recombinase and type II topoisomerase similar to prokaryotic FtsK DNA translocase (Iyer et al., 2004; Chelikani et al., 2014a,b). Studies have shown that the FtsK motor operates as a hexamer during genome segregation (Massey et al., 2006) and it is suggested that the hexamer could be a functionally active form of the Mimivirus packaging ATPase (member of NCLDV). The directionality of the FtsK motor movement is provided by the interaction of the γ domain with a short, 8-base-pair DNA sequence known as KOPS (FtsK Orienting Polar Sequence, 5′-GGGNAGGG-3′) (Bigot et al., 2005). The γ domain also has a KRKA amino acid loop that is required for the interaction with XerD recombinase (Sivananthan et al., 2009). The Mimivirus packaging ATPase motor also possesses a KRKA motif between residues 227 to 230 toward the C-terminus which could be the potential recombinase interaction site. However, the presence of the KRKA motif is not a conserved feature in NCLDVs. It was also found that potential KOPS-like as well as dif-like sequences are present in the Mimivirus genome (Chelikani et al., 2014b). The Mimivirus packaging motor likely gets activated when it encounters a KOPS-like sequence and might recruit topoisomerase II, and this complex is directed to the recombinase already bound at the dif-site. The complex so formed resolves the catenated genome and generates an individual unit length of a genome that could still be circular or near circular. Topoisomerase II and recombinase might leave the complex as these proteins could hinder the efficient translocation of the viral genome by packaging ATPase motor.
Incorporating viruses into soil ecology: A new dimension to understand biogeochemical cycling
Published in Critical Reviews in Environmental Science and Technology, 2023
Xiaolong Liang, Mark Radosevich, Jennifer M. DeBruyn, Steven W. Wilhelm, Regan McDearis, Jie Zhuang
Protozoa and eukaryotic algae are two major divisions of protists and are abundantly and widely distributed in near-surface soil, with algae primarily dwelling in surface soils (Jassey et al., 2022). Viruses that infect protists are highly diverse, including small RNA viruses and nucleocytoplasmic large DNA viruses, have been identified (Coy et al., 2018). Perhaps most notable and receiving the most investigative attention has been the discovery of the first “giant virus”; the amebae infecting Mimivirus, identified in a water-cooling tower (La Scola et al., 2003). The amoebal giant viruses appear specialized in infecting acanthamoeba species and have also been found in soil environments (Rigou et al., 2022). For additional details see reviews by (Schulz et al., 2022; Wilhelm et al., 2017).
Selection, purification, and characterization of a HER2-targeting soluble designed ankyrin repeat protein by E. coli surface display using HER2-positive melanoma cells
Published in Preparative Biochemistry & Biotechnology, 2018
Xiaofei Chen, Xiaoxiao Yu, Xiaoda Song, Li Liu, Yuting Yi, Wenbing Yao, Xiangdong Gao
Here, we provided a simple method for the generation of HER2-targeting DARPin. A DARPin library was built from mimivirus, a kind of giant virus. The library was displayed on E. coli to conduct the live cell sorting on HER2-positive/negative cells.[15,16] After three rounds of screening, a DARPin was selected and purified. The production yield of selected DARPin was about 70 mg/L in a soluble form. The affinity of selected DARPin with HER2 subdomain I was evaluated by flow cytometry and microscale thermophoresis (MST). The kd value between selected DARPin and HER2 was 1.05 ± 0.47 µM. The in vitro experiment showed the capacity of selected DARPin to inhibit tumor cell growth. At a concentration of 640 nM, the selected DARPin could inhibit the growth of SK-BR-3 at a rate of 46.34% in 72 hr by MTT assay. Therefore, we demonstrated that E. coli display combining with selection on live cells was a dependable method for the selection of antibody mimetic DARPin and provided a drug candidate for cancer therapy.