Latest Research News on genomics : Dec 2021

Functional Genomics of P450S

Plant systems utilize a diverse array of cytochrome P450 monooxygenases (P450s) in their biosynthetic and detoxicative pathways. Those P450s in biosynthetic pathways play critical roles in the synthesis of lignins, UV protectants, pigments, defense compounds, fatty acids, hormones, and signaling molecules. Those in catabolic pathways participate in the breakdown of endogenous compounds and toxic compounds encountered in the environment. Because of their roles in this wide diversity of metabolic processes, plant P450 proteins and transcripts can serve as downstream reporters for many different biochemical pathways responding to chemical, developmental, and environmental cues. This review focuses initially on defining P450 biochemistries, nomenclature systems, and the relationships between genes in the extended P450 superfamily that exists in all plant species. Subsequently, it focuses on outlining the many approaches being used to assign function to individual P450 proteins and gene loci. The examples of assigned P450 activities that are spread throughout this review highlight the importance of understanding and utilizing P450 sequences as markers for linking biochemical pathway responses to physiological processes.[1]

From genomics to proteomics

Proteomics is the study of the function of all expressed proteins. Tremendous progress has been made in the past few years in generating large-scale data sets for protein–protein interactions, organelle composition, protein activity patterns and protein profiles in cancer patients. But further technological improvements, organization of international proteomics projects and open access to results are needed for proteomics to fulfil its potential.[2]

Comparative and functional genomics of closteroviruses

The largest extant RNA genomes are found in two diverse families of positive-strand RNA viruses, the animal Coronaviridae and the plant Closteroviridae. Comparative analysis of the viruses from the latter family reveals three levels of gene conservation. The most conserved gene module defines RNA replication and is shared with plant and animal viruses in the alphavirus-like superfamily. A module of five genes that function in particle assembly and transport is a hallmark of the family Closteroviridae and was likely present in the ancestor of all three closterovirus genera. This module includes a homologue of Hsp70 molecular chaperones and three diverged copies of the capsid protein gene. The remaining genes show dramatic variation in their numbers, functions, and origins among closteroviruses within and between the genera. Proteins encoded by these genes include suppressors of RNA silencing, RNAse III, papain-like proteases, the AlkB domain implicated in RNA repair, Zn-ribbon-containing protein, and a variety of proteins with no detectable homologues in the current databases. The evolutionary processes that have shaped the complex and fluid genomes of the large RNA viruses might be similar to those that have been involved in evolution of genomic complexity in other divisions of life.[3]

Genome-wide Characterization of MicroRNAs from Mungbean (Vigna radiata L.)

Aims: MicroRNAs (miRNAs) are endogenous, short (~21-nucleotide), non-coding RNA molecules that play important roles in post-transcriptional gene silencing by directing target mRNA cleavage or translational inhibition. The main aim of this study is to identify and characterize miRNAs from economically important and high stress tolerant crop mungbean (Vigna radiata L.).

Study Design: Conserved miRNAs and their targets were characterized from mungbean using computational and RT-PCR approach.

Place and Duration of Study: Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata- 700054, India between January 2011- November 2015.

Methodology: Conserved miRNAs and their targets from mungbean were identified in this study using homology based strict filtering approach. Software tools such as mfold and psRNATarget were used during this study. Predicted mungbean miRNAs were validated by RT-PCR technique.

Results: In this study using recently published draft genome sequence of mungbean (Vigna radiata  L.) and applying  genome-wide computational-based approaches a total of 56 potentially conserved microRNAs belonging to 28 families were identified. 3 putative mungbean miRNAs (vra-miR160a, vra-miR162b and vra-miR398b) were successfully validated by RT-PCR. Using psRNATarget tool a total of 88 potential miRNA target transcripts were also recognized for the identified mungbean miRNAs which include a number of transcription factors.

Conclusion: For the first time 56 conserved microRNAs and 88 potential target sequences were identified in mungbean. Predicted target transcripts were found to be involved in development, metabolism and stress responses.[4]

Genetics to Genomics in Clinical Medicine

Biomedical research and knowledge has grown exponentially since the completion of the Human Genome Project in the year 2000. There has been a gradual shift from ‘genetics’ (study of genes) to ‘genomics’ (study of the whole genome) in medicine. Advances such as sequencing of the human genome, genome enrichment, epigenetics and bioinformatics have transformed the face of translational research and are beginning to have a major impact on clinical practice. In order to take advantage of the full potential of genomic research in clinical practice, clinicians will need to understand and embrace a significant conceptual shift from ‘Mendelian genetics’ to ‘Post Mendelian genomics’.

A relative lack of genetics to genomics knowledge has been reported amongst senior physicians in major health plans in the United States. This is also true of physicians practicing in the United Kingdom as reflected in the reports by the British Royal Society (BRS), Wellcome Trust and UK department of Health. While large sections of the academic medical community is driving this conceptual shift, a significant proportion of practicing clinicians are not actively involved in these developments. Here we describe the continuum from genetics to genomics in medicine by giving a brief overview of the shift from single gene disorders and chromosomal aberrations to functional genomics and our current understanding of the more dynamic relationship between genotype and phenotype. [5]

Reference

[1] Schuler, M.A. and Werck-Reichhart, D., 2003. Functional genomics of P450s. Annual review of plant biology, 54(1), pp.629-667.

[2] Tyers, M. and Mann, M., 2003. From genomics to proteomics. Nature, 422(6928), pp.193-197.

[3] Dolja, V.V., Kreuze, J.F. and Valkonen, J.P., 2006. Comparative and functional genomics of closteroviruses. Virus research, 117(1), pp.38-51.

[4] Paul, S. and Pal, A., 2017. Genome-wide Characterization of MicroRNAs from Mungbean (Vigna radiata L.). Biotechnology Journal International, pp.1-9.

[5] Sawhney, V., Schilling, R. and Brien, B.O., 2014. Genetics to genomics in clinical medicine. Journal of Advances in Medicine and Medical Research, pp.4926-4938.