Peptide aptamers: selection strategies, mechanisms, and applications in engineered geminivirus resistance

Geminiviruses are circular single-stranded DNA viruses that infect a wide range of plant species and cause 18%–100% yield loss in various economically important crops. Geminiviruses belong to the family Geminiviridae that has been classified into nine genera based on their genome organization, trans-replication of genomic components, vector and host range, coat-protein features, etc. Due to the proliferation of geminiviruses worldwide, there are major problems with their high evolution, recombination, and emergence rate for managing geminivirus diseases. Conventional breeding and genetic engineering-based transgenics approaches are the main strategies applied toward geminivirus resistance. Conventionally, many disease resistance strategies containing control of the insect vector and resistant cultivar are available to control geminiviruses. In addition, a variety of nonconventional strategies based on genetic engineering tools have been utilized in geminivirus resistance strategies. The limitation of conventional breeding is the availability of natural resistance sources, resistance traits in nature, and the time required for a breeding program. In genetic engineering approaches, antisense RNAs, RNA interference constructs, and mutant viral proteins are based on viral sequences. Many of these strategies do not confer high levels of resistance or are limited to cognate and closely related viruses. In the geminivirus life cycle, the viral genome replicates (Rep) by a form of rolling-circle mechanism called recombination-dependent replication, which requires both viral and host proteins. Peptide aptamers are artificial short peptides (8–20 amino acids) with specific binding affinity for target molecules leading to their insertion into a protein scaffold that constrains conformation. This novel approach is due to advancements in technology that utilize peptide aptamers for controlling plant viruses. They can interfere with both protein–protein and, protein–DNA binding, allowing them to target viral protein, which often depends on these interactions for replication. In geminivirus, the Rep protein is a multifunctional protein that is the sole encoded viral protein required for replication. Geminiviruses contain Rep protein, which is one of the conserved features. Thus some of the studies reported the peptide aptamer-based approach for broad-spectrum resistance against geminivirus is used to target viral Rep protein. A variety of existing peptide aptamer selection methods have been introduced in vivo and in vitro. A yeast two-hybrid system is commonly utilized for the selection and screening of peptide aptamers against viral proteins in plants. In comparison with antibodies, this peptide aptamer strategy also offers additional advantages because of the obstacles related to the expression of antibodies in the plant cytoplasm. Overall, the presented applications of peptide aptamers that inhibit the replication of plant viruses might be supporting this technology to develop durable resistance against geminivirus diseases in crops. In this chapter, we will offer an overview of the principle, peptide aptamers selection strategies, mechanisms of action by peptide aptamers, and the applications of peptide aptamers as a potential viral diseases controlling tool with a focus on geminivirus resistance in crop plants.