Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs

Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics–based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m−2·s−1, respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence

What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply?

Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production. Although male sterility is caused by S cytoplasm (male-sterility inducing mitochondria), the action of S cytoplasm is suppressed by restorer-of-fertility (Rf), a nuclear gene. Hence, the genetics of Rf has attained particular interest among plant breeders. The genetic model posits Rf diversity in which an Rf specifically suppresses the cognate S cytoplasm. Molecular analysis of Rf loci in plants has identified various genes; however, pentatricopeptide repeat (PPR) protein (a specific type of RNA-binding protein) is so prominent as the Rf-gene product that Rfs have been categorized into two classes, PPR and non-PPR. In contrast, several shared features between PPR- and some non-PPR Rfs are apparent, suggesting the possibility of another grouping. Our present focus is to group Rfs by molecular genetic classes other than the presence of PPRs. We propose three categories that define partially overlapping groups of Rfs: association with post-transcriptional regulation of mitochondrial gene expression, resistance gene-like copy number variation at the locus, and lack of a direct link to S-orf (a mitochondrial ORF associated with CMS). These groups appear to reflect their own evolutionary background and their mechanism of conferring S cytoplasm specificity

A Lineage-Specific Paralog of Oma1 Evolved into a Gene Family from Which a Suppressor of Male Sterility-Inducing Mitochondria Emerged in Plants

Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognateMS-inducing mitochondria.Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf encodes a protein resemblingOma1,which is involved in the quality control ofmitochondria. In this study, we investigated the molecular evolution of Oma1 homologs in plants.We analyzed 37 plant genomes and concluded that a single copy is the ancestral state in Caryophyllales. Among the sugar beet Oma1 homologs, the orthologous copy is located in a syntenic region that is preserved in Arabidopsis thaliana. The sugar beet Rf is a complex locus consisting of a smallOma1homolog family (RF-Oma1 family) unique to sugar beet. The gene arrangement in the vicinity of the locus is seen in some but not allCaryophyllalean plants and is absent fromAr. thaliana. This suggests a segmental duplication rather than a whole-genome duplication as themechanism of RF-Oma1 evolution.Of thirty-seven positively selected codons in RF-Oma1, twentysix of these sites are located in predicted transmembrane helices. Phylogenetic network analysis indicated that homologous recombination among the RF-Oma1 members played an important role to generate protein activity related to suppression. Together, our data illustrate how an evolutionarily young Rf has emerged from a lineage-specific paralog. Interestingly, several evolutionary features are sharedwith the RNA-binding protein type Rfs.Hence, the evolution of the sugar beet Rf is representative of Rf evolution in general

Male Sterility-Inducing Mitochondrial Genomes: How Do They Differ?

Twenty-nine mitochondrial genomes from 19 angiosperm species have been completely sequenced and have been found to vary in genome size and gene content. Seven of these mitochondrial genomes are known to induce cytoplasmic male sterility (CMS), and thus can be utilized for hybrid seed production or the prevention of pollen dispersal. Genome rearrangement frequently is observed in MS-inducing mitochondria, but it also occurs as part of the normal inter- or intraspecific variation in male fertile (MF) mitochondria. Sequence analyses have revealed that the repertoire of genuine genes is indistinguishable between MS-inducing and MF mitochondria. Deleterious mutations appear to be rare in MS-inducing mitochondria, which may be consistent with the lack of systemic manifestation of CMS. On the other hand, several nucleotide substitutions remain to be investigated for their potential mild effects. Various mitochondrial ORFs are associated with CMS (CMS-ORFs). There are some common but not strict features shared by CMS-ORFs such as their uniqueness to the CMS mitochondrial genome, their association with genes for ATPase subunits, and the hydrophobic nature of their putative translation products. It should be noted that some CMS-ORFs do not satisfy all of these criteria, and ORFs that satisfy these criteria are not necessarily associated with CMS. Therefore, it is difficult to infer the capability of MS induction of mitochondrial genomes solely from their nucleotide sequences. Morphological, physiological, and molecular biological studies suggest that multiple mechanisms cause CMS. Nuclear genes that suppress CMS have been identified. Post-transcriptional suppression of CMS-ORFs mediated by a certain class of RNA binding proteins (pentatrico peptide repeat proteins) is the predominant mechanism of fertility restoration. On the other hand, CMS suppression that is not associated with post-transcriptional suppression of CMS-ORFs has also been reported, suggesting that various types of gene-products are involved in fertility restoration

An apple atp9 pseudogene is maintained at high copy number in 'Golden Delicious'-type mitochondria but is present substoichiometrically in 'Delicious'-type mitochondria

In this study, the mitochondrial atp9 gene sequence of an apple cultivar 'Golden Delicious' was found to exist in one intact version and two truncated versions (termed φatp9-1 and φatp9-2). Interestingly, the φatp9-1 sequence is maintained at high copy number in the six 'Golden Delicious'-cytotype cultivars examined but present substoichiometrically in eight 'Delicious'-cytotype cultivars. Our data also suggest that φatp9-1 originated in a homologous recombination event mediated by the short repeat in a common ancestral mitochondrial genome of 'Golden Delicious' and 'Delicious', and was preferentially amplified in an evolutionary lineage that gave rise to the 'Golden Delicious'-type genome. On the other hand, φatp9-2 was revealed to be present in high abundance in all 14 cultivars examined

An intact mitochondrial cox1 gene and a pseudogene with different genomic configurations are present in apple cultivars 'Golden Delicious' and 'Delicious': Evolutionary aspects

We have characterized the mitochondrial cox1 gene copies in two apple cultivars 'Golden Delicious' and 'Delicious'. Both the cultivars contained an intact copy and a truncated copy of cox1. The intact 'Golden Delicious' and 'Delicious' cox1 genes, designated G-cox1 and D-cox1, respectively, were both found to be actually transcribed to give an RNA of approximately 1.7 kb. The two intact cox1 and two truncated copies (G-φcox1 and D-φcox1) shared a common 1115-bp segment flanked by four combinations of two different 5'- and 3'-sequences. PCR assay demonstrated that the configurations bearing G-cox1 and G-φcox1 existed in substoichiometric amounts within the mitochondrial genome of 'Delicious' whereas substoichiometric molecules carrying D-φcox1 were present in the 'Golden Delicious' mitochondrial genome. Although ancestor/descendant relationships cannot be inferred between the G-cox1 and D-cox1 arrangements, the results led us to hypothesize that (1) the 1115-bp segment containing part of the progenitor cox1 was duplicated, thereby generating a pseudo-cox1 copy, and (2) this was followed by homologous recombination across a portion of the 1115-bp repeats which gave rise to the descendant cox1 and pseudo-cox1 arrangements

Molecular basis of cytoplasmic male sterility in beets : an overview

Sugarbeet cultivars are almost exclusively hybrids, which are produced using the sole source of cytoplasmic male sterility (CMS), the so-called Owen CMS. Several alternative sources of CMS have been described. One of these, I-12CMS(3), was derived from wild beets collected in Pakistan, and another CMS source, GCMS, has a cytoplasmic origin in wild sea beets from France. During the past decade, male sterility-associated mitochondrial genes have been identified in these three CMS systems. Moreover, the recent development of a variety of DNA markers has permitted the genetic mapping of nuclear restorer-of-fertility genes for both Owen and GCMS. This review focuses on the mechanism of CMS in beets