Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation

Proteins are biosynthesized from N to C terminus before they depart from the ribosome and reach their bioactive state in the cell. At present, very little is known about the evolution of conformation and the free energy of the nascent protein with chain elongation. These parameters critically affect the extent of folding during ribosome‐assisted biosynthesis. Here, we address the impact of vectorial amino acid addition on the burial of nonpolar surface area and on the free energy of native‐like structure formation in the absence of the ribosomal machinery. We focus on computational predictions on proteins bearing the globin fold, which is known to encompass the 3/3, 2/2, and archaeal subclasses. We find that the burial of nonpolar surface increases progressively with chain elongation, leading to native‐like conformations upon addition of the last C‐terminal residues, corresponding to incorporation of the last two helices. Additionally, the predicted folding entropy for generating native‐like structures becomes less unfavorable at nearly complete chain lengths, suggesting a link between the late burial of nonpolar surface and water release. Finally, the predicted folding free energy takes a progressive favorable dip toward more negative values, as the chain gets longer. These results suggest that thermodynamic stabilization of the native structure of newly synthesized globins during translation in the cell is significantly enhanced as the chain elongates. This is especially true upon departure of the last C‐terminal residues from the ribosomal tunnel, which hosts ca., 30–40 amino acids. Hence, we propose that release from the ribosome is a crucial step in the life of single‐domain proteins in the cell. Proteins 2014; 82:2318–2331. © 2014 Wiley Periodicals, Inc.     

13C脉冲标记法：不同生育期水稻光合碳在植物-土壤系统中的分配

定量生育期内植物光合碳在植物组织-土壤的分配规律,对于理解全球碳循环有着重要意义。采用~(13)C-CO_2脉冲标记结合室内培养,通过元素分析仪-稳定同位素联用(Flash HT-IRMS)分析植物各部分及土壤δ~(13)C值,比较了不同生育期下水稻光合碳在不同组织间的分配规律,并量化了水稻光合碳向土壤碳库的转移。结果表明:(1)水稻地上部和根系干物质量随水稻生育期的增加而呈现递增趋势,不同的生育期表现为:分蘖期拔节期抽穗期扬花期成熟期。而整个生育期的根冠比为0.2—0.4,分蘖期的根冠比最高,随着水稻生育期的增加而递减,到抽穗期以后根冠比稳定在0.2左右。(2)脉冲标记6h后,水稻地上部和地下部(根系)的δ~(13)C值在-25.52‰—-28.33‰,不同器官的δ~(13)C值存在明显分馏效应,且趋势基本一致,即茎杆(籽粒)叶片(根系);这种由于水稻生育期特性导致的各器官碳同位素分馏的现象,可用于指示不同生育期下水稻光合碳的分配和去向。(3)不同生育期~(13)C-光合碳在植物-土壤系统的分配规律不同,生长前期光合碳向根系及土壤中分配的比例高,具有较强的碳汇能力,而随生育期光合碳在根系及土壤中的分配比例呈下降趋势,但积累量不断增加。(4)不同生育期~(13)C光合碳在水稻-土壤系统中的分配比例差异明显。水稻分蘖期有近30%光合碳用于根系建成并部分通过根系分泌物进入土壤有机碳库(10%),而到成熟期则向籽粒中分配较多,而且光合碳在土壤中的分配比例也随生育期呈下降趋势。研究结果对稻田土壤有机碳循环过程和调控机制的揭示具有重要的理论意义。     

Lack of adequate seed supply is a major bottleneck for effective ecosystem restoration in Chile: friendly amendment to Bannister et al. (2018)

We argue that the need for a quality seed supply chain is a major bottleneck for the restoration of Chile's native ecosystems, thus supplementing the list of bottlenecks proposed by Bannister et al. in 2018. Specifically, there is a need for defining seed transfer zones, developing standards and capacities for properly collecting and storing seeds, reducing information gaps on seed physiology and longevity, and implementing an efficient seed supply chain with certification of seed origin and quality. Without such capacities, countries are unlikely to meet their restoration commitments. Although we focus on bottlenecks in Chile, the issues we raise are relevant to other countries and thus the global agenda for ecological restoration.     

EFFECTS OF LIGHT ON PHOTOSYNTHESIS,GRAZING, AND POPULATION DYNAMICS OF THE HETEROTROPHIC DINOFLAGELLATE PFIESTERIA PISCICIDA (DINOPHYCEAE)1

In studying how environmental factors control the population dynamics of Pfiesteria piscicida Steidinger et Burkholder, we examined the influence of light regime on kleptoplastidic photosynthesis, growth, and grazing. Prey (Rhodomonas sp.)‐saturated growth rate of P. piscicida increased (0.67 ± 0.03 d^?1 to 0.91 ± 0.11 d^?1) with light intensity varying from 0 to 200 μmol photons·m^?2·s^?1. No significant effect was observed on grazing, excluding the possibility that light enhanced P. piscicida growth through stimulating grazing. Light‐grown P. piscicida exhibited a higher gross growth efficiency (0.78 ± 0.10) than P. piscicida incubated in the dark (0.32 ± 0.16), and photosynthetic inhibitors significantly decreased growth of recently fed populations. These results demonstrate a role of kleptoplastidic photosynthesis in enhancing growth in P. piscicida. However, when the prey alga R. sp. was depleted, light's stimulating effect on P. piscicida growth diminished quickly, coinciding with rapid disappearance of Rhodomonas‐derived pigments and RUBISCO from P. piscicida cells. Furthermore, the effect of light on growth was reversed after extended starvation, and starved light‐grown P. piscicida declined at a rate significantly greater than dark‐incubated cultures. The observed difference in rates of decline appeared to be attributable to light‐dependent cannibalism. Using a 5‐chloromethylfluorescein diacetate staining technique, cannibalistic grazing was observed after 7 days of starvation, at a rate four times greater under illumination than in the dark. The results from this study suggest that kleptoplastidy enhances growth of P. piscicida only in the presence of algal prey. When prey is absent, P. piscicida populations may become vulnerable to light‐stimulated cannibalism.