Costa, C. T.; Strieder, M. L.; Abel, S.; Delatorre, C. A. Phosphorus and nitrogen interaction: loss of QC identity in response to P or N limitation is antecipated in pdr23 mutant Braz J Plant Physiol 23, 219-229, (2011) DOI: 10.1590/S1677-04202011000300006
Changes in root architecture are an important
adaptive strategy used by plants in response to limited nutrient
availability to increase the odds of acquiring them. The quiescent
center (QC) plays an important role by altering the meristem activity
causing differentiation and therefore, inducing a determinate growth
program. The arabidopsis mutant pdr23 presents primary short root in the
presence of nitrate and is inefficient in the use of nucleic acids as a
source of phosphorus. In this study the effect of the pdr23 mutation on
the QC maintenance under low phosphorus (P) and/or nitrogen is
evaluated. QC identity is maintained in wild-type in the absence of
nitrate and/or phosphate if nucleic acids can be used as an alternative
source of these nutrients, but not in pdr23. The mutant is not able to
use nucleic acids efficiently for substitute Pi, determinate growth is
observed, similar to wild-type in the total absence of P. In the absence
of N pdr23 loses the expression of QC identity marker earlier than
wild-type, indicating that not only the response to P is altered, but
also to N. The data suggest that the mutation affects a gene involved
either in the crosstalk between these nutrients or in a pathway shared
by both nutrients limitation response. Moreover loss of QC identity is
also observed in wild-type in the absence of N at longer limitation.
Less drastic symptoms are observed in lateral roots of both genotypes.
Phosphate (Pi) and its anhydrides constitute
major nodes in metabolism. Thus, plant performance depends directly on
Pi nutrition. Inadequate Pi availability in the rhizosphere is a common
challenge to plants, which activate metabolic and developmental
responses to maximize Pi usage and acquisition. The sensory mechanisms
that monitor environmental Pi and transmit the nutritional signal to
adjust root development have increasingly come into focus. Recent
transcriptomic analyses and genetic approaches have highlighted complex
antagonistic interactions between external Pi and Fe bioavailability and
have implicated the stem cell niche as a target of Pi sensing to
regulate root meristem activity.
Kopycki, J.; Schmidt, J.; Abel, S.; Grubb, C. D. Chemoenzymatic synthesis of diverse
thiohydroximates from glucosinolate-utilizing enzymes from Helix pomatia
and Caldicellulosiruptor saccharolyticus Biotechnol Lett 33, 1039-1046, (2011) DOI: 10.1007/s10529-011-0530-y
Thiohydroximates comprise a diverse class of compounds important in both biological and industrial chemistry. Their syntheses are generally limited to simple alkyl and aryl compounds with few stereocenters and a narrow range of functional groups. We hypothesized that sequential action of two recombinant enzymes, a sulfatase from Helix pomatia and a β-O-glucosidase from Caldicellulosiruptor saccharolyticus, on glucosinolates would allow synthesis of thiohydroximates from a structurally broad array of abundant precursors. We report successful synthesis of thiohydroximates of varied chemical classes, including from homochiral compounds of demonstrated biological activity. The chemoenzymatic synthetic route reported here should allow access to many, if not all, of the thiohydroximate core structures of the ~200 known naturally occurring glucosinolates. The enrichment of this group for compounds with possible pharmacological potential is discussed.
Delker, C.; Quint, M. Expression level polymorphisms: heritable traits shaping natural variation Trends Plant Sci 16, 481-488, (2011) DOI: 10.1016/j.tplants.2011.05.009
Natural accessions of many species harbor a wealth of genetic variation visible in a large array of phenotypes. Although expression level polymorphisms (ELPs) in several genes have been shown to contribute to variation in diverse traits, their general impact on adaptive variation has likely been underestimated. At present, ELPs have predominantly been correlated to quantitative trait loci (eQTLs) that occupy central hubs in signaling networks, which pleiotropically affect numerous traits. To increase the sensitivity of detecting minor effect eQTLs or those that act in a trait-specific manner, we emphasize the need for more systematic approaches. This requires, but is not limited to, refining experimental designs such as reduction of tissue complexity and combinatorial methods including a priori defined networks.
Schumann, N.; Navarro-Quezada, A.; Ullrich, K.; Kuhl, C.; Quint, M. Molecular Evolution and Selection Patterns of Plant F-box Proteins with C-terminal Kelch Repeats Plant Physiol 155, 835-850, (2011) DOI: 10.1104/pp.110.166579
The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization.
Asquini, E.; Gerdol, M.; Gasperini, D.; Igic, B.; Graziosi, G.; Pallavicini, A. S-RNase-like Sequences in Styles of Coffea (Rubiaceae). Evidence for S-RNase Based Gametophytic Self-Incompatibility? Trop Plant Biol 4, 237-249, (2011) DOI: 10.1007/s12042-011-9085-2
Although RNase-based self-incompatibility (SI)
is suspected to operate in a wide group of plant families, it has been
characterized as the molecular genetic basis of SI in only three
distantly related families, Solanaceae, Plantaginaceae, and Rosaceae,
all described over a decade ago. Previous studies found that
gametophytic SI, controlled by a multi-allelic S-locus, operates in the
coffee family (Rubiaceae). The molecular genetic basis of this mechanism
remains unknown, despite the immense importance of coffee as an
agricultural commodity. Here, we isolated ten sequences with features of
T2-S-type RNases from two Coffea species. While three of the sequences
were identified in both species and clearly do not appear to be S-locus
products, our data suggest that six sequences may be S-alleles in the
self-incompatible C. canephora, and one may be a relict in the
self-compatible C. arabica. We demonstrate that these sequences show
style-specific expression, display polymorphism in C. canephora, and
cluster with S-locus products in a phylogenetic analysis that includes
other plant families with RNase-based SI. Although our results are not
definitive, in part because the available plant materials were limited
and data patterns relatively complex, our results strongly hint that
RNase-based SI mechanism operates in the Rubiaceae family.
Carbonell, A.; Flores, R.; Gago, S.
Trans -cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid RNA Nucleic Acids Research 39, 2432-2444, (2011) DOI: 10.1093/nar/gkq1051
Trans -cleaving hammerheads with discontinuous or extended stem I and with tertiary stabilizing motifs (TSMs) have been tested previously against short RNA substrates in vitro at low Mg 2+ concentration. However, the potential of these ribozymes for targeting longer and structured RNAs in vitro and in vivo has not been examined. Here, we report the in vitro cleavage of short RNAs and of a 464-nt highly structured RNA from potato spindle tuber viroid (PSTVd) by hammerheads with discontinuous and extended formats at submillimolar Mg 2+ . Under these conditions, hammerheads derived from eggplant latent viroid and peach latent mosaic viroid (PLMVd) with discontinuous and extended formats, respectively, where the most active. Furthermore, a PLMVd-derived hammerhead with natural TSMs showed activity in vivo against the same long substrate and interfered with systemic PSTVd infection, thus reinforcing the idea that this class of ribozymes has potential to control pathogenic RNA replicons.
Flores, R.; Grubb, C.D.; Elleuch, A.; Nohales, M.A; Delgado, S.; Gago, S. Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus RNA Biol 8(2), 200-206, (2011) DOI: 10.4161/rna.8.2.14238
Viroids and viroid-like satellite RNAs from plants, and the human hepatitis delta virus (HDV) RNA share some properties that include small size, circularity and replication through a rolling-circle mechanism. Replication occurs in different cell compartments (nucleus, chloroplast and membrane-associated cytoplasmatic vesicles) and has three steps: RNA polymerization, cleavage and ligation. The first step generates oligomeric RNAs that result from the reiterative transcription of the circular templates of one or both polarities, and is catalyzed by either the RNA-dependent RNA polymerase of the helper virus on which viroid-like satellite RNAs are functionally dependent, or by host DNA-dependent RNA polymerases that, remarkably, viroids and HDV redirect to transcribe RNA templates. Cleavage is mediated by host enzymes in certain viroids and viroid-like satellite RNAs, while in others and in HDV is mediated by cis-acting ribozymes of three classes. Ligation appears to be catalyzed mainly by host enzymes. Replication most likely also involves many other non-catalytic proteins of host origin and, in HDV, the single virus-encoded protein.