Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p‐Coumaric acid and related aromatic acids

Lignin comprises 15–25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP‐binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p‐coumarate, 3‐phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X‐ray crystal structures of protein–ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin‐derived aromatic compounds. The screens and structural data provide new functional assignments for these solute‐binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence‐based functional annotation methods for this family of proteins.Proteins 2013; 81:1709–1726. © 2013 Wiley Periodicals, Inc.     

Progress toward a biomimetic leaf: 4,000 h of hydrogen production by coating‐stabilized nongrowing photosynthetic Rhodopseudomonas palustris

Intact cells are the most stable form of nature's photosynthetic machinery. Coating‐immobilized microbes have the potential to revolutionize the design of photoabsorbers for conversion of sunlight into fuels. Multi‐layer adhesive polymer coatings could spatially combine photoreactive bacteria and algae (complementary biological irradiance spectra) creating high surface area, thin, flexible structures optimized for light trapping, and production of hydrogen (H₂) from water, lignin, pollutants, or waste organics. We report a model coating system which produced 2.08 ± 0.01 mmol H₂ m^?2 h^?1 for 4,000 h with nongrowing Rhodopseudomonas palustris, a purple nonsulfur photosynthetic bacterium. This adhesive, flexible, nanoporous Rps. palustris latex coating produced 8.24 ± 0.03 mol H₂ m^?2 in an argon atmosphere when supplied with acetate and light. A simple low‐pressure hydrogen production and trapping system was tested using a 100 cm² coating. Rps. palustris CGA009 was combined in a bilayer coating with a carotenoid‐less mutant of Rps. palustris (CrtI^?) deficient in peripheral light harvesting (LH2) function. Cryogenic field emission gun scanning electron microscopy (cryo‐FEG‐SEM) and high‐pressure freezing were used to visualize the microstructure of hydrated coatings. A light interaction and reactivity model was evaluated to predict optimal coating thickness for light absorption using the Kubelka‐Munk theory (KMT) of reflectance and absorptance. A two‐flux model predicted light saturation thickness with good agreement to observed H₂ evolution rate. A combined materials and modeling approach could be used for guiding cellular engineering of light trapping and reactivity to enhance overall photosynthetic efficiency per meter square of sunlight incident on photocatalysts. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

增强UV-B辐射对暖温带落叶阔叶林土庄绣线菊水分利用效率、气孔导度、叶氮素含量及形态特性的影响

在北京东灵山暖温带森林生态系统中,选择常见灌丛土庄绣线菊(Spiraea pubescens),建立UV-B控制实验。连续3个生长季每天增补9.4 kJ·m^-2的辐射剂量,模拟臭氧衰减17%时近地表面UV-B辐射的增强。该实验的目的是在野外环境下观测,长时间人工增强UV-B辐射对土庄绣线菊叶片的气孔导度、碳同位素比率(δ¹³C)、叶含水量、叶面积、特别是水分利用效率(WUE)和叶片全氮含量等指标的影响。实验结果表明,增强UV-B辐射显著减少了土庄绣线菊的叶面积(50.1%),提高了叶片全氮含量(102%)。同时,UV-B辐射还在一定程度上(尽管统计显示不显著)降低了气孔导度(16.1%)、胞间CO₂浓度与大气CO₂浓度之比(C_i/C_a) (4.0%)、提高了碳同位素比率(δ¹³C)(20.5‰)、叶含水量(3.1%)及比叶重(SLW)(5.2%),从而导致WUE的增加(4.1%)和植物的抗旱能力增强。值得注意的是,深层土壤(30~40 cm)含水量变化会影响气孔导度、δ¹³C和WUE对紫外辐射的响应程度:在土壤干旱的季节(6月和9月),气孔导度、δ¹³C、WUE这些指标处理和对照的差异很小,但是当土壤水分充足时(7月和8月),处理和对照的差异就较为显著。另外,随着实验处理时间的延长,UV-B的效应变得不显著。相关分析表明,UV-B辐射降低了土壤含水量(30~40 cm)与土庄绣线菊叶含水量、δ¹³C、C_i/C_a和气孔导度的相关系数,增强了WUE与土壤含水量的相关性,这也许是由于UV-B辐射增强了WUE对土壤水分变化的敏感性。该研究的结果表明UV-B辐射对土庄绣线菊的形态和生长有显著的影响,但对主要水分生理指标影响不显著。     

Can Managers Bank on Seed Banks When Restoring Pinus taeda L. Plantations in Southwest Georgia?

In the southeastern United States, private forestland managers are under increased pressure to provide wildlife habitat and biodiversity in addition to commercial products such as timber. This study used a stand classification scheme based on vegetation biodiversity from Hedman et al. to compare seed bank composition of benchmark (BM) and nonbenchmark (NBM) Loblolly pine ( Pinus taeda ) stands. In the Hedman et al. study, BM stands contained species associated with Longleaf pine ( P. palustris )/Wiregrass ( Aristida stricta ) communities, whereas NBM stands contained species associated with disturbed sites. The current vegetation of the BM and NBM stands had an average cover of 7.9%/m² and an average richness of 11 species/m². The intent for this study was to assist in understanding the potential role of the seed bank during stand development and restoration. We collected seed bank samples from six pine plantations in the winter of 2006. Seed bank samples yielded 2,885 germinants representing 56 unique species but only 4 were found in both current herbaceous vegetation plots and seed bank. The seed bank was dominated by native dicots. In BM stands, 76% of species were native, whereas in NBM stands, 69% were native. Seed bank samples from NBM stands had greater species richness ( p = 0.03) and total germinants ( p = 0.03) than BM stands. Although the seed bank in all stands was dominated by native species, our data suggest that the seed bank under P. taeda stands should not be viewed as the sole source of native species for most restoration goals.     

Bayou virus detected in non‐oryzomyine rodent hosts: an assessment of habitat composition,reservoir community structure,and marsh rice rat social dynamics

In the United States, Bayou virus (BAYV) ranks second only to Sin Nombre virus (SNV) in terms of hantavirus pulmonary syndrome (HPS) incidents, having been confirmed in cases from Texas and Louisiana since its discovery in 1994. This study on BAYV infection among sympatric, non‐oryzomyine rodents (“spillover”) in Freeport, TX, is the first to link patterns of hantavirus interspecific spillover with the spatiotemporal ecology of the primary host (marsh rice rat, Oryzomys palustris). Mark‐recapture and/or harvest methods were employed from March 2002 through May 2004 in two macrohabitat types. Rodent blood samples were screened for the presence of IgG antibody to BAYV antigen by IFA after which Ab‐positive blood, saliva, and urine were analyzed for the presence of viral RNA by nested RT‐PCR. From 727 non‐oryzomyine captures, five seropositive (but not viral RNA positive) individuals were detected: one each of Baiomys taylori, Peromyscus leucopus, and Reithrodontomys fulvescens; and two Sigmodon hispidus. Spillover hosts were not associated with macrohabitat where O. palustris abundance, density, or seroprevalence was highest. Rather, spillover occurred in the macrohabitat indicative of greater overall disturbance (as indicated by grazing and exotic plant diversity) and overall biodiversity. Spillover occurred during periods of high seroprevalence detected elsewhere within the study region. Spillover locations differed significantly from all other capture locations in terms of percent water, shrub, and grass cover. Although greater habitat and mammal diversity of old‐fields may serve to reduce seroprevalence levels by tempering intraspecific contacts between rice rats, greater diversity also may create an ecologically opportunistic setting for BAYV spillover. Impacts of varying levels of disturbance and biodiversity on transmission dynamics represent a vastly uncharacterized component of the evolutionary ecology of hantaviruses.     

甜菜夜蛾对氰戊菊酯和顺式氯氰菊酯的抗性机理

通过对活体增效作用进行测定和生化分析,探讨了甜菜夜蛾对氰戊菊酯和顺式氯氰菊酯的抗性机理.结果表明:增效醚(PBO)、增效磷(SV1)、磷酸三苯酯(TPP)和顺丁烯二酸二乙酯(DEM)对甜菜夜蛾抗氰戊菊酯品系(Fen-R)和敏感品系(S)的增效倍数之比分别为10.2、7.8、12.5和1.1,对抗顺式氯氰菊酯品系(Cyp-R)和敏感品系(S)的增效倍数之比分别为21.6、15.5、8.6和1.2.PBO、SV1和TPP对氰戊菊酯和顺式氯氰菊酯均有显著增效作用,表明多功能氧化酶和羧酸酯酶均参与了甜菜夜蛾对氰戊菊酯和顺式氯氰菊酯的抗性.Fen-R品系和Cyp-R品系4龄幼虫羧酸酯酶的活性分别是S品系的1.9和2.2倍,而谷胱甘肽-S-转移酶活性与S品系差异不显著,表明羧酸酯酶活性的提高是甜菜夜蛾对氰戊菊酯和顺式氯氰菊酯产生抗性的重要原因,谷胱甘肽-S-转移酶与两种药剂的抗性无关.Fen-R品系和Cyp-R品系的Na-K-ATPase活性与S品系均无显著差异,但在相同浓度下氰戊菊酯和顺式氯氰菊酯对S品系Na-K-ATPase的抑制作用显著高于抗性品系,表明抗性品系Na-K-ATPase对杀虫剂的敏感性已明显降低.     

Conservation of genetic diversity in old‐growth forest communities of the southeastern United States

Question: How do studies of the distribution of genetic diversity of species with different life forms contribute to the development of conservation strategies? Location: Old‐growth forests of the southeastern United States. Methods: Reviews of the plant allozyme literature are used to identify differences in genetic diversity and structure among species with different life forms, distributions and breeding systems. The general results are illustrated by case studies of four plant species characteristic of two widespread old‐growth forest communities of the southeastern United States: the Pinus palustris – Aristida stricta (Longleaf pine – wiregrass) savanna of the Coastal Plain and the Quercus – Carya – Pinus (Oak‐hickory‐pine) forest of the Piedmont. Genetic variation patterns of single‐gene and quantitative traits are also reviewed. Results: Dominant forest trees, represented by Pinus palustris(longleaf pine) and Quercus rubra (Northern red oak), maintain most of their genetic diversity within their populations whereas a higher proportion of the genetic diversity of herbaceous understorey species such as Sarracenia leucophylla and Trillium reliquum is distributed among their populations. The herbaceous species also tend to have more population‐to‐population variation in genetic diversity. Higher genetic differentiation among populations is seen for quantitative traits than for allozyme traits, indicating that interpopulation variation in quantitative traits is influenced by natural selection. Conclusion: Developing effective conservation strategies for one or a few species may not prove adequate for species with other combinations of traits. Given suitable empirical studies, it should be possible to design efficient conservation programs that maintain natural levels of genetic diversity within species of conservation interest.     

Limited costs of wrong root placement in Rumex palustris in heterogeneous soils

Nutrient hot spots in the soil have a limited life span, but the costs and benefits for root foraging are still underexposed. We assessed short-term costs that may arise when a nutrient-rich patch induces root proliferation, but then rapidly disappears. Rumex palustris plants were grown with a homogeneous or a heterogeneous nutrient application. After root proliferation in a nutrient-rich patch, nutrient supply was switched from homogeneous to heterogeneous, and vice versa, or the patch location was changed. R. palustris proliferated its roots in the rich patch. After switching, the relative growth rates of the roots were adjusted to the novel pattern of nutrient availability. However, the changes in local root biomass lagged behind the rapid shift in nutrient supply, because the root mass realized in specific sectors could not be rapidly relocated. Despite this, R. palustris did not exhibit costs of switching in terms of biomass or nitrogen uptake. Our data suggest that rapid shifts in uptake rate and redistribution of nitrogen within the plant may have lowered the costs of incorrect root placement.     

Effects of longleaf pine planting density and other factors on stand structure and associated wildlife habitat

The primary objective of many longleaf pine (Pinus palustris) restoration programs is to enhance or restore habitat for wildlife dependent on herbaceous plant communities. Because herbaceous cover is inversely related to canopy cover, restoration programs often place restrictions on longleaf pine planting density. However, the influence of planting density on understory plant communities has been inadequately evaluated. Therefore, we initiated a study to examine the relative influences of planting density and other factors on overall understory composition and forage availability for white‐tailed deer (Odocoileus virginianus) and northern bobwhite (Colinus virginianus) in nine longleaf pine stands throughout the Coastal Plain of Alabama during 2017–2018. We found that coverage of herbaceous plants decreased 3.5%, coverage of woody plants decreased 2.4%, and coverage of northern bobwhite forage plants decreased 1.9% for each 1 m²/ha increase in longleaf pine basal area. However, planting density was not a significant predictor of current basal area, nor coverage of any functional group of plants we examined, likely because current longleaf pine density averaged only 46% (range = 30–64%) of seedling planting density. We did not detect an effect of prescribed fire on stand condition or understory plant communities, likely due to variability in fire timing and frequency. Our findings related to planting density were likely a function of low longleaf pine survival, which is not uncommon. Because of this and the inherent variability in growth rates for young longleaf pine stands, restoration programs should consider placing greater emphasis on post‐planting monitoring and management than planting density.