Molecular Evolution and Functional Diversification of Replication Protein A1 in Plants

Replication protein A (RPA) is a heterotrimeric, single-stranded DNA binding complex required for eukaryotic DNA replication, repair, and recombination. RPA is composed of three subunits, RPA1, RPA2, and RPA3. In contrast to single RPA subunit genes generally found in animals and yeast, plants encode multiple paralogs of RPA subunits, suggesting subfunctionalization. Genetic analysis demonstrates that five Arabidopsis thaliana RPA1 paralogs (RPA1A to RPA1E) have unique and overlapping functions in DNA replication, repair, and meiosis. We hypothesize here that RPA1 subfunctionalities will be reflected in major structural and sequence differences among the paralogs. To address this, we analyzed amino acid and nucleotide sequences of RPA1 paralogs from 25 complete genomes representing a wide spectrum of plants and unicellular green algae. We find here that the plant RPA1 gene family is divided into three general groups termed RPA1A, RPA1B, and RPA1C, which likely arose from two progenitor groups in unicellular green algae. In the family Brassicaceae the RPA1B and RPA1C groups have further expanded to include two unique sub-functional paralogs RPA1D and RPA1E, respectively. In addition, RPA1 groups have unique domains, motifs, cis-elements, gene expression profiles, and pattern of conservation that are consistent with proposed functions in monocot and dicot species, including a novel C-terminal zinc-finger domain found only in plant RPA1C-like sequences. These results allow for improved prediction of RPA1 subunit functions in newly sequenced plant genomes, and potentially provide a unique molecular tool to improve classification of Brassicaceae species

Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication

Replication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division

High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core "DSB" response specific to clastogenic treatments.

Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as "collateral" damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe(26+) high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the "DSB response" were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing "extended night." This response was not apparent in gamma-irradiated plants

From a Census of 680,000 Street Trees to Smart Stormwater Management: A Study of Efficacy and Economics of Street Tree Guards in New York City

Green Infrastructure (GI) is a strategy of incorporating a distributed network of eco-technical systems that retain and detain stormwater to improve the hydrology of developed landscapes. GI is particularly needed in urban environments where roads, buildings, parking areas, and paved public spaces create a hardscape that results in rainfall rapidly running off and subsequently polluting natural waterways. However, the same dense, built-up environment that necessitates GI also creates a barrier to installing the amount of GI needed to meaningfully alter urban hydrologic behavior. Although a wide array of systems have been developed to fit in different urban niches, as exemplified by sedum green roofs, bioswales, rain gardens, rainwater harvesting, and permeable paving, many can be costly and difficult to integrate at scale. Thus, measuring and optimizing the performance of existing urban vegetation represents an important area of focus for stormwater management and offers potential for more economical use of resources allocated for GI. This paper focuses on examining the role of urban street trees in stormwater management

Green roof seasonal variation: comparison of the hydrologic behavior of a thick and a thin extensive system in New York City

Green roofs have been utilized for urban stormwater management due to their ability to capture rainwater locally. Studies of the most common type, extensive green roofs, have demonstrated that green roofs can retain significant amounts of stormwater, but have also shown variation in seasonal performance. The purpose of this study is to determine how time of year impacts the hydrologic performance of extensive green roofs considering the covariates of antecedent dry weather period (ADWP), potential evapotranspiration (ET0) and storm event size. To do this, nearly four years of monitoring data from two full-scale extensive green roofs (with differing substrate depths of 100 mm and 31 mm) are analyzed. The annual performance is then modeled using a common empirical relationship between rainfall and green roof runoff, with the addition of Julian day in one approach, ET0 in another, and both ADWP and ET0 in a third approach. Together the monitoring and modeling results confirm that stormwater retention is highest in warmer months, the green roofs retain more rainfall with longer ADWPs, and the seasonal variations in behavior are more pronounced for the roof with the thinner media than the roof with the deeper media. Overall, the ability of seasonal accounting to improve stormwater retention modeling is demonstrated; modification of the empirical model to include ADWP, and ET0 improves the model R 2 from 0.944 to 0.975 for the thinner roof, and from 0.866 to 0.870 for the deeper roof. Furthermore, estimating the runoff with the empirical approach was shown to be more accurate then using a water balance model, with model R 2 of 0.944 and 0.866 compared to 0.975 and 0.866 for the thinner and deeper roof, respectively. This finding is attributed to the difficulty of accurately parameterizing the water balance model

Grid-Competitive Residential and Commercial Fully Automated PV Systems Technology: Final technical Report, August 2011

Under DOE's Technology Pathway Partnership program, SunPower Corporation developed turn-key, high-efficiency residential and commercial systems that are cost effective. Key program objectives include a reduction in LCOE values to 9-12 cents/kWh and 13-18 cents/kWh respectively for the commercial and residential markets. Target LCOE values for the commercial ground, commercial roof, and residential markets are 10, 11, and 13 cents/kWh. For this effort, SunPower collaborated with a variety of suppliers and partners to complete the tasks below. Subcontractors included: Solaicx, SiGen, Ribbon Technology, Dow Corning, Xantrex, Tigo Energy, and Solar Bridge. SunPower's TPP addressed nearly the complete PV value chain: from ingot growth through system deployment. Throughout the award period of performance, SunPower has made progress toward achieving these reduced costs through the development of 20%+ efficient modules, increased cell efficiency through the understanding of loss mechanisms and improved manufacturing technologies, novel module development, automated design tools and techniques, and reduced system development and installation time. Based on an LCOE assessment using NREL's Solar Advisor Model, SunPower achieved the 2010 target range, as well as progress toward 2015 targets