ABSTRACT
Genetic imprinting refers to the unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms, including mammals and flowering plants. Although many imprinted genes have been identified in plants, the functions of these imprinted genes have remained largely uninvestigated. We report genome-wide analysis of gene expression, DNA methylation and small RNAs in the rice endosperm and functional tests of five imprinted genes during seed development using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated gene9 (CRISPR/Cas9) gene editing technology. In the rice endosperm, we identified 162 maternally expressed genes (MEGs) and 95 paternally expressed genes (PEGs), which were associated with miniature inverted-repeat transposable elements, imprinted differentially methylated loci and some 21-22 small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs). Remarkably, one-third of MEGs and nearly one-half of PEGs were associated with grain yield quantitative trait loci. Most MEGs and some PEGs were expressed specifically in the endosperm. Disruption of two MEGs increased the amount of small starch granules and reduced grain and embryo size, whereas mutation of three PEGs reduced starch content and seed fertility. Our data indicate that both MEGs and PEGs in rice regulate nutrient metabolism and endosperm development, which optimize seed development and offspring fitness to facilitate parental-offspring coadaptation. These imprinted genes and mechanisms could be used to improve the grain yield of rice and other cereal crops.
Subject(s)
Genes, Plant , Genomic Imprinting , Oryza/embryology , Oryza/genetics , Seeds/embryology , Seeds/genetics , Alleles , CRISPR-Cas Systems/genetics , Crosses, Genetic , DNA Methylation , DNA Transposable Elements/genetics , Endosperm/genetics , Flowers/genetics , Gene Expression Regulation, Plant , Genome-Wide Association Study , Models, Biological , Quantitative Trait Loci/genetics , RNA, Untranslated/genetics , RNA, Untranslated/metabolism , Seeds/anatomy & histologyABSTRACT
Expression of a multidrug resistance transporter renders bacterial cells resistant to a variety of drugs. The major facilitator superfamily (MFS) comprises the largest group of bacterial multidrug transporters. There are over 20 MFS efflux pumps annotated on the genome of Vibrio cholerae, but little is known about their functions and regulation. In this study, five MFS efflux pumps were characterised, each of which is associated with a divergently transcribed putative LysR-type transcriptional regulator (MfsR). It was found that each of these MFS structural genes is regulated by the corresponding MfsR regulator. Deletion of these five mfs genes results in increased susceptibility to tetracycline and crude bile as well as a colonisation defect in an infant mouse colonisation model. Moreover, tetracycline and unknown intestinal signals could serve as co-inducers for the MfsR regulators. These data suggest that MFS efflux pumps are important both for antimicrobial resistance and V. cholerae pathogenesis.
