Hypothetical protein predicted to be tumor suppressor: a protein functional analysis

RNAi screening of uncharacterized genes identifies promising druggable targets in Schistosoma japonicum

Schistosomiasis affects more than 250 million people worldwide and is one of the neglected tropical diseases. Currently, the treatment of schistosomiasis relies on a single drug-praziquantel-which has led to increasing pressure from drug resistance. Therefore, there is an urgent need to find new treatments. The development of genome sequencing has provided valuable information for understanding the biology of schistosomes. In the genome of Schistosoma japonicum, approximately 11% of the protein-coding sequences are uncharacterized genes (UGs) annotated as "hypothetical protein" or "protein of unknown function." These poorly understood genes have been unjustifiably neglected, although some may be essential for the survival of the parasites and serve as potential drug targets. In this study, we systematically mined the highly expressed UGs in both genders of this parasite throughout key developmental stages in their mammalian host, using our previously published S. japonicum genome and RNA-seq data. By employing in vitro RNA interference (RNAi), we screened 126 UGs that lack homologs in Homo sapiens and identified 8 that are essential for the parasite vitality. We further investigated two UGs, Sjc_0002003 and Sjc_0009272, which resulted in the most severe phenotypes. Fluorescence in situ hybridization demonstrated that both genes were expressed throughout the body without sex bias. Silencing either Sjc_0002003 or Sjc_0009272 reduced the cell proliferation in the body. Furthermore, in vivo RNAi indicated both genes are required for the growth and survival of the parasites in the mammalian host. For Sjc_0002003, we further characterize the underlying molecular cause of the observed phenotype. Through RNA-seq analysis and functional studies, we revealed that silencing Sjc_0002003 reduces the expression of a series of intestinal genes, including Sjc_0007312 (hypothetical protein), Sjc_0008276 (vha-17), Sjc_0002942 (PLA2G15), and Sjc_0003646 (SJCHGC09134 protein), leading to gut dilation. Our work highlights the importance of UGs in schistosomes as promising targets for drug development in the treatment of the schistosomiasis.

Putative Protein Discovery from Microalgal Genomes as a Synthetic Biology Protein Library for Heavy Metal Bio-Removal

Simple Summary

Nowadays, heavy metal polluted wastewater is one of the global challenges that leads to an insufficient supply of clean water. Taking advantage of what nature has to offer, several organisms, including microalgae, can natively bioremediate these heavy metals. However, the effectiveness of such processes does not meet expectations, especially with the increasing amount of pollution in today’s world. Therefore, with the goal of creating effective strains, synthetic biology via bioengineering is widely used as a strategy to enhance the heavy metal bio-removing capability, either by directly engineering the native ability of organisms or by transferring the ability to a more suitable host. In order to do so, a list of genes or proteins involved in the processes is crucial for stepwise engineering. Yet, a large amount of information remains to be discovered. In this work, a comprehensive library of putative proteins that are involved in heavy metal bio-removal from microalgae was constructed. Moreover, with the development of machine learning, the 3D structures of these proteins are also predicted, using machine learning-based methods, to aid the use of synthetic biology further.

Abstract

Synthetic biology is a principle that aims to create new biological systems with particular functions or to redesign the existing ones through bioengineering. Therefore, this principle is often utilized as a tool to put the knowledge learned to practical use in actual fields. However, there is still a great deal of information remaining to be found, and this limits the possible utilization of synthetic biology, particularly on the topic that is the focus of the present work—heavy metal bio-removal. In this work, we aim to construct a comprehensive library of putative proteins that might support heavy metal bio-removal. Hypothetical proteins were discovered from Chlorella and Scenedesmus genomes and extensively annotated. The protein structures of these putative proteins were also modeled through Alphafold2. Although a portion of this workflow has previously been demonstrated to annotate hypothetical proteins from whole genome sequences, the adaptation of such steps is yet to be done for library construction purposes. We also demonstrated further downstream steps that allow a more accurate function prediction of the hypothetical proteins by subjecting the models generated to structure-based annotation. In conclusion, a total of 72 newly discovered putative proteins were annotated with ready-to-use predicted structures available for further investigation.