Husna, Amity University Kolkata
Multidrug and toxic compound extrusion (MATE) are protein families that play an important role in various physiological functions of plant growth and development. The MATE gene family is one of the largest families of genes that can encode transporters in plants They can transport secondary metabolites, toxic compounds, and heavy metals; regulate disease resistance, and participate in plant hormone regulation. Although the structure and function of an increasing number of the members of the MATE transporter family have been identified in many plant species like Arabidopsis, soybean, tomato, and sesame; however, this information is still very limited in rice (Oryza Sativa).
A recent study published in BMC Ecology and Evolution used bioinformatic methods for analyzing the chromosome distribution, physical properties, conservation, evolution, and expression patterns of rice MATE family members systematically. This provided a very important theoretical basis for the functional identification of MATE family members.
The following steps were followed to obtain the data of the MATE genome in rice:
1. Identification of the MATE genes within the rice genome
One of the most commonly used methods to predict gene function is Phylogenetic Analysis, which may also provide a reliable reference for further functional verification. So, recent studies divided the rice MATE family into four subfamilies based on the phylogenetic tree.
The MATE genes within the rice genome were identified via homology searches and domain (Pfam: PF01554) prediction. Total 46 genes encoding specific MATE proteins were identified in the rice genome via homology searches and domain prediction. The genes were named OsMATE1–OsMATE46, this naming was done as per the physical location of genes on the chromosome.
2. Analysis of Chromosome distribution and replication pattern of the OsMATE genes
Analysis of OsMATE gene chromosome mapping revealed that the distribution of 46 MATE genes across the 12 chromosomes of rice, was uneven. The distribution is said to be uneven because chromosome 3 contains the largest number of MATE genes-a total of 10, and Chromosome 5 has only 1 MATE gene. Additionally, a high similarity was observed between the protein sequences within each gene cluster. 6 pairs of fragment-repeat genes were detected as well. These results together indicate that tandem repeat and fragment replication of the MATE genes were the main driving force for amplification of the MATE gene family during the evolutionary process and contributed to the extension of the rice MATE gene family.
3. To Characterize cis-regulatory elements within the promoter regions of OsMATE genes
Cis-regulatory elements present in the promoter regions play a very important role in the plant’s response towards stress. 11 putative stress-responsive cis-regulatory elements were identified in 1500 bp upstream of these OsMATE genes. Expression patterns of genes in different tissues were analyzed using RNA-seq and the expression was constitutive.
qRT-PCR based analysis showed differential expression patterns which shows that the stress-related response elements contained in each MATE gene promoter differ and are capable of significantly tolerating the salt and drought stress in rice.
Conclusions are drawn from the study:
The analyzed results of this study provide comprehensive information on the MATE gene family in rice and aids in the understanding of functional divergence of MATE genes. 46 MATE genes were identified within the rice genome and their comparison with homologous genes of other species revealed the potential function of those genes in transport. Pertaining to their important role in plant physiology, MATE transporters could also be ideal targets for breeding programs for the improvement of agricultural-related traits like aluminium tolerance, iron nutrition, and accumulation of secondary metabolites including increasing anthocyanin contents or eliminating toxic alkaloids.
The results of qRT-PCR suggest that members of the rice MATE gene family can respond differently to different stresses and that the MATE genes have different regulatory pathways in response to abiotic stress in rice.
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Source: Du, Zhixuan, et al. “Genome-Wide Characterization of MATE Gene Family and Expression Profiles in Response to Abiotic Stresses in Rice (Oryza Sativa).” BMC Ecology and Evolution, vol. 21, no. 1, July 2021, p. 141. BioMed Central, doi:http://10.1186/s12862-021-01873-y.
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About the Author: Husna is an undergraduate student of BTech Biotechnology at Amity University Kolkata. She is a research enthusiast in Immunology and Immunotherapy but she has a keen interest in various other Bioscience subjects as well. She is constantly focused on improving her knowledge and laboratory skills through various internships. She is a Scientific content writer who has knowledge in diverse backgrounds of Biotechnology.
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