Institute for Integrative Genome Biology

Institute for Integrative Genome Biology

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News Article | April 18, 2017

Katherine Borkovich will be honored June 2 for her research on fungal genomics RIVERSIDE, Calif. (http://www. ) -- Katherine Borkovich, a professor and chair of the UC Riverside Department of Plant Pathology and Microbiology, has been elected a fellow of the American Academy of Microbiology. The academy, the leadership group within the American Society for Microbiology, recognizes excellence, originality, and leadership in the microbiological sciences. She will be recognized at the annual American Society for Microbiology Conference June 2 in New Orleans. Borkovich, who is also a professor at UC Riverside's Institute for Integrative Genome Biology, is focused on functional genomics and the signaling pathways used by filamentous fungi to response to the environment, with the goal of identifying genes that control growth, development and pathogenesis. She is being honored for her research into environmental sensing by heterotrimeric G proteins in fungi, contributions to fungal genomics, leadership of microbiology undergraduate and graduate programs, and for teaching a research-based laboratory course for the microbiology major at UC Riverside. She was instrumental in establishment of the microbiology undergraduate major and reinstatement of the microbiology graduate program at UC Riverside. She was recognized with the 2016 campus Distinguished Teaching Award for her teaching of a research-based course for the Microbiology major, Experimental Microbiology. Borkovich received her Ph.D. from UCLA and did postdoctoral work at the University of Chicago and Caltech.

Ung N.,Institute for Integrative Genome Biology | Lal S.,University of California at Riverside | Smith H.M.S.,Institute for Integrative Genome Biology | Smith H.M.S.,University of California at Riverside
Plant Physiology | Year: 2011

Growth of the aerial part of the plant is dependent upon the maintenance of the shoot apical meristem (SAM). A balance between the self-renewing stem cells in the central zone (CZ) and organogenesis in the peripheral zone (PZ) is essential for the integrity, function, and maintenance of the SAM. Understanding how the SAM maintains a balance between stem cell perpetuation and organogenesis is a central question in plant biology. Two related BELL1-like homeodomain proteins, PENNYWISE (PNY) and POUND-FOOLISH (PNF), act to specify floral meristems during reproductive development. However, genetic studies also show that PNY and PNF regulate the maintenance of the SAM. To understand the role of PNY and PNF in meristem maintenance, the expression patterns for genes that specifically localize to the peripheral and central regions of the SAM were examined in Arabidopsis (Arabidopsis thaliana). Results from these experiments indicate that the integrity of the CZ is impaired in pny pnf plants, which alters the balance of stem cell renewal and organogenesis. As a result, pools of CZ cells may be allocated into initiating leaf primordia. Consistent with these results, the integrity of the central region of pny pnf SAMs can be partially restored by increasing the size of the CZ. Interestingly, flower specification is also reestablished by augmenting the size of the SAM in pny pnf plants. Taken together, we propose that PNYand PNF act to restrict organogenesis to the PZ by maintaining a boundary between the CZ and PZ. © 2011 American Society of Plant Biologists.

Seo J.-K.,Institute for Integrative Genome Biology | Seo J.-K.,National Academy of Agricultural Science | Wu J.,Peking University | Lii Y.,Institute for Integrative Genome Biology | And 2 more authors.
Molecular Plant-Microbe Interactions | Year: 2013

Small RNAs regulate a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity, in a sequence-specific manner. Accumulating evidence reveals that host endogenous small RNAs and small RNA pathway components play important roles in plant immune responses against various pathogens, including bacteria, fungi, oomycetes, and viruses. Small-RNA-mediated defense responses are regulated through diverse pathways and the components of these pathways, including Dicer-like proteins, RNA-dependent RNA polymerases, Argonaute proteins, and RNA polymerase IV and V, exhibit functional specificities as well as redundancy. In this review, we summarize the recent insights revealed mainly through the examination of two model plants, Arabidopsis and rice, with a primary focus on our emerging understanding of how these small RNA pathway components contribute to plant immunity. © 2013 The American Phytopathological Society.

Park S.-Y.,University of California at Riverside | Park S.-Y.,Institute for Integrative Genome Biology | Peterson F.C.,Medical College of Wisconsin | Mosquna A.,University of California at Riverside | And 7 more authors.
Nature | Year: 2015

Rising temperatures and lessening fresh water supplies are threatening agricultural productivity and have motivated efforts to improve plant water use and drought tolerance. During water deficit, plants produce elevated levels of abscisic acid (ABA), which improves water consumption and stress tolerance by controlling guard cell aperture and other protective responses. One attractive strategy for controlling water use is to develop compounds that activate ABA receptors, but agonists approved for use have yet to be developed. In principle, an engineered ABA receptor that can be activated by an existing agrochemical could achieve this goal. Here we describe a variant of the ABA receptor PYRABACTIN RESISTANCE 1 (PYR1) that possesses nanomolar sensitivity to the agrochemical mandipropamid and demonstrate its efficacy for controlling ABA responses and drought tolerance in transgenic plants. Furthermore, crystallographic studies provide a mechanistic basis for its activity and demonstrate the relative ease with which the PYR1 ligand-binding pocket can be altered to accommodate new ligands. Thus, we have successfully repurposed an agrochemical for a new application using receptor engineering. We anticipate that this strategy will be applied to other plant receptors and represents a new avenue for crop improvement. ©2015 Macmillan Publishers Limited. All rights reserved.

News Article | April 14, 2016

The researchers cautioned that this is a preliminary study with a small sample size. Future research would expand to include a greater number of gardens, and focus on characteristics of the corn, such as tolerance to drought, difference in cob size and flowering time. The research addresses the importance of maintaining a diverse range of genetic resources for future crop improvement. A broad mix of genetic material is useful for breeding modern improved lines, minimizing the vulnerability of inbred crops to pathogens and pests, improving performance and incorporating unique traits. Yet, crop genetic diversity is threatened in developing and developed countries as policies and program encourage the use of relatively homogeneous modern cultivars and as people migrate from farms to cities, often abandoning farming altogether. "As genetic diversity erodes, we stand on a chair with shaky legs," said Norman C. Ellstrand, a professor of genetics at UC Riverside and co-author of the paper, "Maize Germplasm Conservation in Southern California's Urban Gardens: Introduced Diversity Beyond ex situ and in situ Management," was published online in the journal Economic Botany. Ellstrand, who is also a member of UC Riverside's Institute for Integrative Genome Biology and interim director of the university's new "broad-sense" agriculture institute, CAFÉ (California Agriculture and Food Enterprise), co-authored the paper with Joanne Heraty, a former UC Davis graduate student who Ellstrand supervised. She is now a project manager for the Yolo County Resource Conservation District. In 2008, the researchers collected corn samples from home gardens and community gardens in Los Angeles and Riverside. They genetically compared the garden populations to five commercially available varieties of corn that included two horticultural varieties, two industrial varieties used in large scale agricultural crop plantings and one bulk bin variety purchased from Big Saver Foods supermarket in Riverside. They included the supermarket variety because farmers indicated that local ethnic markets were sometimes a source of seed for their gardens. Southern California is an ideal location to study joint human and plant migration because immigrants from Mexico and Central America frequently maintain plots of crops from their homelands in home gardens and community gardens. Past research has shown that corn genetic diversity is being eroded, particularly in Mexico and conservation strategies tend to fall into two categories: ex situ and in situ. Ex situ refers to using a controlled environment, such as a gene bank or botanical garden, to maintain genetic resources. In situ refers to a farmer-based approach via traditional agricultural practices like seed saving and selective breeding. Ellstrand and Heraty describe home and community gardens in Southern California as providing a third method, which combines ex situ and in situ methods of conservation and is aided by human migration. "People collect baseball cards and people collect plant seeds," Ellstrand said. "In reality, it is not all that surprising that as people move around they help preserve the genetic diversity of plants." More information: Joanne M. Heraty et al. Maize Germplasm Conservation in Southern California's Urban Gardens: Introduced Diversity Beyond ex situ and in situ Management, Economic Botany (2016). DOI: 10.1007/s12231-016-9333-3

Tsuchiya T.,Institute for Integrative Genome Biology | Eulgem T.,Institute for Integrative Genome Biology
Plant Signaling and Behavior | Year: 2014

Recently we reported that the Arabidopsis thaliana PHD-finger protein EDM2 (enhanced downy mildew 2) impacts disease resistance by affecting levels of di-methylated lysine 9 of histone H3 (H3K9me2) at an alternative polyadenylation site in the immune receptor gene RPP7. EDM2-dependent modulation of this post-translational histone modification (PHM) shifts the balance between full-length RPP7 transcripts and prematurely polyadenylated transcripts, which do not encode the RPP7 protein. Our previous work genetically linked, for the first time, PHM s to alternative polyadenylation and established EDM2 as a critical component mediating PHM-dependent polyadenylation control. However, how EDM2 is recruited to its genomic target sites and how it affects H3K9me2 levels is unknown. Here we show the PHD-finger module of EDM2 to recognize histone H3 bearing certain combinations of 3 distinct PHM s. Our results suggest that targeting of EDM2 to specific genomic regions is mediated by the histone-binding selectivity of its PHD-finger domain. © 2014 Landes Bioscience.

Weiberg A.,Institute for Integrative Genome Biology | Jin H.,Institute for Integrative Genome Biology
Current Opinion in Plant Biology | Year: 2015

Eukaryotic regulatory small RNAs (sRNAs) that induce RNA interference (RNAi) are involved in a plethora of biological processes, including host immunity and pathogen virulence. In plants, diverse classes of sRNAs contribute to the regulation of host innate immunity. These immune-regulatory sRNAs operate through distinct RNAi pathways that trigger transcriptional or post-transcriptional gene silencing. Similarly, many pathogen-derived sRNAs also regulate pathogen virulence. Remarkably, the influence of regulatory sRNAs is not limited to the individual organism in which they are generated. It can sometimes extend to interacting species from even different kingdoms. There they trigger gene silencing in the interacting organism, a phenomenon called cross-kingdom RNAi. This is exhibited in advanced pathogens and parasites that produce sRNAs to suppress host immunity. Conversely, in host-induced gene silencing (HIGS), diverse plants are engineered to trigger RNAi against pathogens and pests to confer host resistance. Cross-kingdom RNAi opens up a vastly unexplored area of research on mobile sRNAs in the battlefield between hosts and pathogens. © 2015 Elsevier Ltd.

Ung N.,Institute for Integrative Genome Biology | Smith H.M.S.,Institute for Integrative Genome Biology
Plant Signaling and Behavior | Year: 2011

Shoot growth and development is mediated by the activity of the shoot meristem, which initiates leaves and axillary meristems. Meristem maintenance is achieved by a poorly understood process that functions to sustain the balance of stem cell perpetuation in the central zone (CZ) and organogenesis in the peripheral zone (PZ). A recent study showed that two related homeodomain transcription factors, PENNYWISE (PNY) and POUND-FOOLISH (PNF), regulate meristem maintenance by controlling the integrity of the CZ. The non-flower producing phenotype displayed by pny pnf plants can be rescued by genetically increasing the size of the shoot meristem. In this addendum, we show that augmenting the size of the central region of pny pnf shoot meristems partially rescues the meristem termination phenotype that occurs during early stages of vegetative development. Thus, regulation of CZ integrity by PNY and PNF is crucial for vegetative and reproductive development. © 2011 Landes Bioscience.

PubMed | Institute for Integrative Genome Biology
Type: Journal Article | Journal: Plant physiology | Year: 2016

A sensitive and dynamically responsive auxin signaling reporter based on the DII domain of the INDOLE-3-ACETIC ACID28 (IAA28, DII) protein from Arabidopsis (Arabidopsis thaliana) was modified for use in maize (Zea mays). The DII domain was fused to a yellow fluorescent protein and a nuclear localization sequence to simplify quantitative nuclear fluorescence signal. DII degradation dynamics provide an estimate of input signal into the auxin signaling pathway that is influenced by both auxin accumulation and F-box coreceptor concentration. In maize, the DII-based marker responded rapidly and in a dose-dependent manner to exogenous auxin via proteasome-mediated degradation. Low levels of DII-specific fluorescence corresponding to high endogenous auxin signaling occurred near vasculature tissue and the outer layer and glume primordia of spikelet pair meristems and floral meristems, respectively. In addition, high DII levels were observed in cells during telophase and early G1, suggesting that low auxin signaling at these stages may be important for cell cycle progression.

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