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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
Viruses are composed of a protein capsid containing a DNA or RNA genome. Some viruses also include a lipid envelope, but the majority do not. The size of virus particles that infect prokaryotes (i.e., bacteriophages or phages) varies widely but most have viral capsid diameter ranging from 20 nm to 70 nm and the length up to 200 nm in the tailed phages. On the smaller end of the range, a single-stranded DNA phage, vBRpoMi-Mini, was observed by Zhan and Chen (2019) to have a 22 nm diameter and contains only four open reading frames in its genome. Viruses are the smallest biological agents in soil, and their volume is generally 8000–125,000 times smaller than the volume of bacterial cells (Kuzyakov & Mason-Jones, 2018). Some groups of viruses may be much larger than phages. The “giant viruses”, a unique group of nucleocytoplasmic large DNA viruses (NCLVDs) that are commonly found in aquatic environments, but were recently found in soil (Legendre et al., 2014; Rigou et al., 2022). Giant viruses have large particle sizes, ranging from around 100 nm to over 300 nm, and genome length up to ∼400 kb.
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
In this study, ankyrin repeats from giant DNA viruses were used to generate antibody mimetic DARPins. Giant viruses are dsDNA viruses. The genome sizes of giant viruses are similar to those of small bacteria. Unlike other viruses, they also have many uncharacteristic features. For example, there are some genes resemble cellular genes involved in translation, DNA repair, polysaccharide synthesis, and protein folding.[18] Also, some genes that were used to believe only existed in cellular life to synthesize proteins have been discovered in giant viruses, which is a challenge to the traditional definition of viruses.[19] Thus, a kind of giant virus, mimivirus, was chosen to be the origin of the AR consensus sequence. Through the analysis of mimivirus putative ankyrin repeat protein, the consensus sequence was extracted. Combined with the reported N and C-terminal cap, a DARPin sequence was established as listed in Figure 1a. X in the sequence stands for the random amino acids on the interaction surface. Swiss Model verified that the secondary structure of designed mimivirus-based protein was the same as those reported in most articles(Figure 1b).[6,7] There were three AR domains flanked by the terminal caps, each AR domain contained four designed random sites in one side of the proteins’ secondary structure. The random sites located in the groove of the protein secondary structure surface. Thus, DARPins could interact with different targets by different amino acids in the random sites. As the skeleton structures of DARPins were rigid, the interaction would not change the structures of DARPins. The bound of DARPins to targets had the characteristic of high specificity.