Tobacco (Nicotiana tabacum) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene-space sequence reads from the tobacco nuclear genome and report the detailed analysis of more than 2,500 tobacco transcription factors (TFs). The tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes, indicating that evolution of the Solanaceae was not associated with the gain or loss of TF families. However, we found notable differences between tobacco and non-Solanaceae species in TF family size and evidence for both tobacco- and Solanaceae-specific subfamily expansions. Compared with TF families from sequenced plant genomes, tobacco has a higher proportion of ERF/AP2, C2H2 zinc finger, homeodomain, GRF, TCP, zinc finger homeodomain, BES, and STERILE APETALA (SAP) genes and novel subfamilies of BES, C2H2 zinc finger, SAP, and NAC genes. The novel NAC subfamily, termed TNACS, appears restricted to the Solanaceae, as they are absent from currently sequenced plant genomes but present in tomato (Solanum lycopersicum), pepper (Capsicum annuum), and potato (Solanum tuberosum). They constitute approximately 25% of NAC genes in tobacco. Based on our phylogenetic studies, we predict that many of the more than 50 tobacco group IX ERF genes are involved in jasmonate responses. Consistent with this, over two-thirds of group IX ERF genes tested showed increased mRNA levels following jasmonate treatment. Our data are a major resource for the Solanaceae and fill a void in studies of TF families across the plant kingdom.

Plants continually monitor their innate developmental status and external environment and make adjustments to balance growth, differentiation and stress responses using a complex and highly interconnected regulatory network composed of various signaling molecules and regulatory proteins. Phytohormones are an essential group of signaling molecules that work through a variety of different pathways conferring plasticity to adapt to the everchanging developmental and environmental cues. Of these, jasmonic acid (JA), a lipid-derived molecule, plays an essential function in controlling many different plant developmental and stress responses. In the past decades, significant progress has been made in our understanding of the molecular mechanisms that underlie JA metabolism, perception, signal transduction and its crosstalk with other phytohormone signaling pathways. In this review, we discuss the JA signaling pathways starting from its biosynthesis to JA-responsive gene expression, highlighting recent advances made in defining the key transcription factors and transcriptional regulatory proteins involved. We also discuss the nature and degree of crosstalk between JA and other phytohormone signaling pathways, highlighting recent breakthroughs that broaden our knowledge of the molecular bases underlying JA-regulated processes during plant development and biotic stress responses.

Seven races of Striga gesnerioides parasitic on cowpea, a major food and forage legume in sub-Saharan Africa, have been identified. Race-specific resistance of cowpea to Striga involves a coiled-coil nucleotide binding site leucine-rich repeat domain resistance protein encoded by the RSG3-301 gene. Knockdown of RSG3-301 expression by virus-induced gene silencing in the multirace-resistant cowpea cultivar B301 results in the failure of RSG3-301-silenced plants to mount a hypersensitive response and promotes parasite necrosis when challenged with Striga race SG3, whereas the resistance response to races SG2 and SG5 is unaltered. Our findings indicate that a gene-for-gene resistance mechanism is operating in these unique plant-plant associations.

Momilactones are bioactive diterpenoids that contribute to plant defense against pathogens and allelopathic interactions between plants. Both cultivated and wild grass species ofOryzaandEchinochloa crus-galli(barnyard grass) produce momilactones using a biosynthetic gene cluster (BGC) in their genomes. The bryophyteCalohypnum plumiforme(formerlyHypnum plumaeforme) also produces momilactones, and the bifunctional diterpene cyclase geneCpDTC1/HpDTC1,which is responsible for the production of the diterpene framework, has been characterized. To understand the molecular architecture of the momilactone biosynthetic genes in the moss genome and their evolutionary relationships with other momilactone-producing plants, we sequenced and annotated theC. plumiformegenome. The data revealed a 150-kb genomic region that contains two cytochrome P450 genes, theCpDTC1/HpDTC1gene and the “dehydrogenase momilactone A synthase” gene tandemly arranged and inductively transcribed following stress exposure. The predicted enzymatic functions in yeast and recombinant assay and the successful pathway reconstitution inNicotiana benthamianasuggest that it is a functional BGC responsible for momilactone production. Furthermore, in a survey of genomic sequences of a broad range of plant species, we found that momilactone BGC is limited to the two grasses (OryzaandEchinochloa) andC. plumiforme, with no synteny among these genomes. These results indicate that while the gene cluster inC. plumiformeis functionally similar to that in rice and barnyard grass, it is likely a product of convergent evolution. To the best of our knowledge, this report of a BGC for a specialized plant defense metabolite in bryophytes is unique.

The Solanaceae are an economically important family of plants that include tobacco (Nicotiana tabacum L.), tomato, and potato. Drought is a major cause of crop losses. We have identified major changes in physiology, metabolites, mRNA levels, and promoter activities during the tobacco response to drought. We have classified these as potential components of core responses that may be common to many plant species or responses that may be family/species-specific features of the drought stress response in tobacco or the Solanaceae. In tobacco the largest increase in any metabolite was a striking 70-fold increase in 4-hydroxy-2-oxoglutaric acid (KHG) in roots that appears to be tobacco/Solanaceae specific. KHG is poorly characterized in plants but is broken down to pyruvate and glyoxylate after the E. coli SOS response to facilitate the resumption of respiration. A similar process in tobacco would represent a mechanism to restart respiration upon water availability after drought. At the mRNA level, transcription factor gene induction by drought also showed both core and species/family specific responses. Many Group IX Subgroup 3 AP2/ERF transcription factors in tobacco appear to play roles in nicotine biosynthesis as a response to herbivory, whereas their counterparts in legume species appear to play roles in drought responses. We observed apparent Solanaceae-specific drought induction of several Group IId WRKY genes. One of these, NtWRKY69, showed ABA-independent drought stress-inducible promoter activity that moved into the leaf through the vascular tissue and then eventually into the surrounding leaf cells. We propose components of a core metabolic response to drought stress in plants and also show that some major responses to drought stress at the metabolome and transcriptome levels are family specific. We therefore propose that the observed family-specific changes in metabolism are regulated, at least in part, by family-specific changes in transcription factor activity. We also present a list of potential targets for the improvement of Solanaceae drought responses.