KEY MESSAGE : Bulk segregant analysis coupled with whole genome sequencing is a powerful approach and cost-effective method to identify loci controlling fruit traits in tomato. Domestication of fruit ...and vegetable crops was accompanied by selection for weight of the edible parts. Increases in fruit weight are controlled by multiple quantitative trait loci (QTL). To date, only two fruit weight genes have been cloned and a third has been fine-mapped. Genes that control locule number also impact fruit weight and two of them are known. To efficiently identify additional tomato fruit weight (FW) and locule number (LC) loci, six F₂ populations were generated from crosses between closely related tomato accessions for which the alleles of the cloned FW and LC genes were known. We employed the bulk segregant approach coupled to whole genome sequencing (QTL-seq) which led to the identification of three highly significant and newly mapped FW QTL. fw11.2 was located in the distal part of chromosome 11 above the known loci fas and fw11.3; fw1.1 in the pericentromeric region of chromosome 1; and fw3.3 located ~1.6 Mb below the known fruit weight gene, SlKLUH/FW3.2. In addition, we mapped three LC QTL (lcn2.4, lcn5.1, and lcn6.1) although their significance was generally low. To confirm the location of the gene underlying fw11.2, we developed additional markers and conducted progeny tests. These results allowed us to narrow down the fw11.2 QTL to a region of ~750 kb corresponding to 66 candidate genes. Our research approach provided a cost-effective and time-efficient method for the identification of additional genes involved in FW and LC that could be used for both fruit development studies and crop improvement programs.
Members of the plant-specific gene families IQD/SUN, OFP and YABBY are thought to play important roles in plant growth and development. YABBY family members are involved in lateral organ polarity and ...growth; OFP members encode transcriptional repressors, whereas the role of IQD/SUN members is less clear. The tomato fruit shape genes SUN, OVATE, and FASCIATED belong to IQD/SUN, OFP and the YABBY gene family, respectively. A gene duplication resulting in high expression of SUN leads to elongated fruit, whereas a premature stop codon in OVATE and a large inversion within FASCIATED control fruit elongation and a flat fruit shape, respectively. In this study, we identified 34 SlSUN, 31 SlOFP and 9 SlYABBY genes in tomato and identified their position on 12 chromosomes. Genome mapping analysis showed that the SlSUN, SlOFP, and SlYABBY genes were enriched on the top and bottom segments of several chromosomes. In particular, on chromosome 10, a cluster of SlOFPs were found to originate from tandem duplication events. We also constructed three phylogenetic trees based on the protein sequences of the IQ67, OVATE and YABBY domains, respectively, from members of these families in Arabidopsis and tomato. The closest putative orthologs of the Arabidopsis and tomato genes were determined by the position on the phylogenetic tree and sequence similarity. Furthermore, expression analysis showed that some family members exhibited tissue-specific expression, whereas others were more ubiquitously expressed. Also, certain family members overlapped with known QTLs controlling fruit shape in Solanaceous plants. Combined, these results may help elucidate the roles of SUN, OFP and YABBY family members in plant growth and development.
Abstract Chronic diseases are the leading cause of death and disability worldwide, and many of these conditions are linked to chronic inflammation. One potential cause of chronic inflammation is an ...increased intestinal epithelial permeability. Recent studies have demonstrated that parasympathetic stimulation via the efferent abdominal vagus nerve increases the expression and proper localization of tight junction proteins and decreases intestinal epithelial permeability. This finding may provide a novel approach for treating and preventing many chronic conditions. Importantly, physical activity is associated with increased resting parasympathetic (vagal) activity and lower risk of chronic diseases. However, high intensity long duration exercise can be harmful to overall health. Specifically, individuals who frequently exercise strenuously and for longer time intervals have the same mortality rates as sedentary individuals. This may be explained, in part, by longer periods of reduced vagal activity as vagal activity is markedly reduced both during and after intense exercise. We hypothesize that one mechanism by which exercise provides its health benefits is by increasing resting vagal activity and decreasing intestinal epithelial permeability, thus decreasing chronic inflammation. Additionally, we hypothesize that long periods of reduced vagal activity in individuals who exercise at high intensities and for longer durations, decrease the integrity of the intestinal barrier, putting them at greater risk of chronic inflammation and a host of chronic diseases. Thus, this hypothesis provides a conceptual link between the well-established benefits of frequent exercise and the paradoxical deleterious effects of prolonged, high-intensity exercise without adequate rest.
SUN controls elongated tomato (Solanum lycopersicum) shape early in fruit development through changes in cell number along the different axes of growth. The gene encodes a member of the IQ domain ...family characterized by a calmodulin binding motif. To gain insights into the role of SUN in regulating organ shape, we characterized genome-wide transcriptional changes and metabolite and hormone accumulation after pollination and fertilization in wild-type and SUN fruit tissues. Pericarp, seed/placenta, and columella tissues were collected at 4, 7, and 10 d post anthesis. Pairwise comparisons between SUN and the wild type identified 3,154 significant differentially expressed genes that cluster in distinct gene regulatory networks. Gene regulatory networks that were enriched for cell division, calcium/transport, lipid/hormone, cell wall, secondary metabolism, and patterning processes contributed to profound shifts in gene expression in the different fruit tissues as a consequence of high expression of SUN. Promoter motif searches identified putative cis-elements recognized by known transcription factors and motifs related to mitotic-specific activator sequences. Hormone levels did not change dramatically, but some metabolite levels were significantly altered, namely participants in glycolysis and the tricarboxylic acid cycle. Also, hormone and primary metabolite networks shifted in SUN compared with wild-type fruit. Our findings imply that SUN indirectly leads to changes in gene expression, most strongly those involved in cell division, cell wall, and patterning-related processes. When evaluating global coregulation in SUN fruit, the main node represented genes involved in calcium-regulated processes, suggesting that SUN and its calmodulin binding domain impact fruit shape through calcium signaling.
Phosphagen kinases (PKs) are known to be distributed throughout the animal kingdom, but have recently been discovered in some protozoan and bacterial species. Within animal species, these enzymes ...play a critical role in energy homeostasis by catalyzing the reversible transfer of a high-energy phosphoryl group from Mg⋅ATP to an acceptor molecule containing a guanidinium group. In this work, a putative PK gene was identified in the oomycete Phytophthora sojae that was predicted, based on sequence homology, to encode a multimeric hypotaurocyamine kinase. The recombinant P. sojae enzyme was purified and shown to catalyze taurocyamine phosphorylation efficiently (kcat/KM (taurocyamine)=2×105M−1s−1) and glycocyamine phosphorylation only weakly (kcat/KM (glycocyamine)=2×102M−1s−1), but lacked any observable kinase activity with the more ubiquitous guanidinium substrates, creatine or arginine. Additionally, the enzyme was observed to be dimeric but lacked cooperativity between the subunits in forming a transition state analog complex. These results suggest that protozoan PKs may exhibit more diversity in substrate specificity than was previously thought.
Arginine kinases catalyze the reversible transfer of a high-energy phosphoryl group from ATP to L-arginine to form phosphoarginine, which is used as an energy buffer in insects, crustaceans, and some ...unicellular organisms. It plays an analogous role to that of phosphocreatine in vertebrates. Recently, putative arginine kinases were identified in several bacterial species, including the social Gram-negative soil bacterium Myxococcus xanthus. It is still unclear what role these proteins play in bacteria and whether they have evolved to acquire novel functions in the species in which they are found. In this study, we biochemically purified and characterized a putative M. xanthus arginine kinase, Ark, and demonstrated that it has retained the ability to catalyze the phosphorylation of arginine by using ATP. We also constructed a null mutation in the ark gene and demonstrated its role in both certain stress responses and development.
SUNcontrols elongated tomato (Solanum lycopersicum) shape early in fruit development through changes in cell number along the different axes of growth. The gene encodes a member of the IQ domain ...family characterized by a calmodulin binding motif. To gain insights into the role of SUN in regulating organ shape, we characterized genome-wide transcriptional changes and metabolite and hormone accumulation after pollination and fertilization in wild-type and SUN fruit tissues. Pericarp, seed/placenta, and columella tissues were collected at 4, 7, and 10 d post anthesis. Pairwise comparisons between SUN and the wild type identified 3,154 significant differentially expressed genes that cluster in distinct gene regulatory networks. Gene regulatory networks that were enriched for cell division, calcium/transport, lipid/hormone, cell wall, secondary metabolism, and patterning processes contributed to profound shifts in gene expression in the different fruit tissues as a consequence of high expression ofSUN. Promoter motif searches identified putative cis-elements recognized by known transcription factors and motifs related to mitotic-specific activator sequences. Hormone levels did not change dramatically, but some metabolite levels were significantly altered, namely participants in glycolysis and the tricarboxylic acid cycle. Also, hormone and primary metabolite networks shifted in SUN compared with wild-type fruit. Our findings imply that SUN indirectly leads to changes in gene expression, most strongly those involved in cell division, cell wall, and patterning-related processes. When evaluating global coregulation in SUN fruit, the main node represented genes involved in calcium-regulated processes, suggesting that SUN and its calmodulin binding domain impact fruit shape through calcium signaling.
High expression of a gene that controls tomato shape is accompanied by dramatic shifts in gene expression and metabolite and hormone accumulation during the early stages of fruit development.
SUN
...controls elongated tomato (
Solanum lycopersicum
) shape early in fruit development through changes in cell number along the different axes of growth. The gene encodes a member of the IQ domain family characterized by a calmodulin binding motif. To gain insights into the role of SUN in regulating organ shape, we characterized genome-wide transcriptional changes and metabolite and hormone accumulation after pollination and fertilization in wild-type and SUN fruit tissues. Pericarp, seed/placenta, and columella tissues were collected at 4, 7, and 10 d post anthesis. Pairwise comparisons between SUN and the wild type identified 3,154 significant differentially expressed genes that cluster in distinct gene regulatory networks. Gene regulatory networks that were enriched for cell division, calcium/transport, lipid/hormone, cell wall, secondary metabolism, and patterning processes contributed to profound shifts in gene expression in the different fruit tissues as a consequence of high expression of
SUN
. Promoter motif searches identified putative cis-elements recognized by known transcription factors and motifs related to mitotic-specific activator sequences. Hormone levels did not change dramatically, but some metabolite levels were significantly altered, namely participants in glycolysis and the tricarboxylic acid cycle. Also, hormone and primary metabolite networks shifted in SUN compared with wild-type fruit. Our findings imply that SUN indirectly leads to changes in gene expression, most strongly those involved in cell division, cell wall, and patterning-related processes. When evaluating global coregulation in SUN fruit, the main node represented genes involved in calcium-regulated processes, suggesting that SUN and its calmodulin binding domain impact fruit shape through calcium signaling.
Abstract only
Phosphagen kinases (PK) are a family of enzymes that catalyze the reversible transfer of a high‐energy gamma phosphoryl group from ATP to a guanidino acceptor molecule. A novel ...hypotaurocyamine kinase (HTK) from the protozoan oomycete
Phytophthora sojae
(PsPK) was studied to determine substrate specificity, oligomerization state, and cooperativity. Isothermal titration calorimetry was used to determine the kinetic constants of PsPK reacting with taurocyamine and, less strongly, glycocyamine by titrating the guanidino substrate at varying concentrations into a solution containing the HTK and MgATP. The K
m
for taurocyamine and MgATP was found to be 0.59 mM and 3.78 mM, respectively, with a k
cat
of 34.66 s
−1
, while the K
m
for glycocyamine and MgATP was found to be 5.1 mM and 5.1 mM, respectively, with a k
cat
of 3.2 s
−1
. Size exclusion chromatography indicates PsPK is an oligomer and isothermal titration calorimetry suggests no cooperativity among subunits. Our results coupled with findings in
Monosiga
suggest oligomerization evolved first in the protozoa and that cooperativity sometime later. The data also indicate there is diverse substrate specificity in protozoan PKs previously thought to exist only in annelida. This project was made possible by the support of USDA grant (USDA 2011‐68004‐30104) and the Howard Hughes Medical Institute Undergraduate Science Education Program.
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