The complex response of free and bound amino acids to water stress during the seed setting stage in Arabidopsis

Free amino acids (FAAs) and protein‐bound amino acids (PBAAs) in seeds play an important role in seed desiccation, longevity, and germination. However, the effect that water stress has on these two functional pools, especially when imposed during the crucial seed setting stage is unclear. To better understand these effects, we exposed Arabidopsis plants at the seed setting stage to a range of water limitation and water deprivation conditions and then evaluated physiological, metabolic, and proteomic parameters, with special focus on FAAs and PBAAs. We found that in response to severe water limitation, seed yield decreased, while seed weight, FAA, and PBAA content per seed increased. Nevertheless, the composition of FAAs and PBAAs remained unaltered. In response to severe water deprivation, however, both seed yield and weight were reduced. In addition, major alterations were observed in both FAA and proteome compositions, which indicated that both osmotic adjustment and proteomic reprogramming occurred in these naturally desiccation‐tolerant organs. However, despite the major proteomic alteration, the PBAA composition did not change, suggesting that the proteomic reprogramming was followed by a proteomic rebalancing. Proteomic rebalancing has not been observed previously in response to stress, but its occurrence under stress strongly suggests its natural function. Together, our data show that the dry seed PBAA composition plays a key role in seed fitness and therefore is rigorously maintained even under severe water stress, while the FAA composition is more plastic and adaptable to changing environments, and that both functional pools are distinctly regulated.     

Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2

Pacific geoducks (Panopea generosa) are clams found along the northeast Pacific coast where they are important components of coastal and estuarine ecosystems and a major aquaculture product. The Pacific coastline, however, is also experiencing rapidly changing ocean habitat, including significant reductions in pH. To better understand the physiological impact of ocean acidification on geoduck clams, we characterized for the first time the proteomic profile of this bivalve during larval development and compared it to that of larvae exposed to low pH conditions. Geoduck larvae were reared at pH 7.5 (ambient) or pH 7.1 in a commercial shellfish hatchery from day 6 to day 19 postfertilization and sampled at six time points for an in‐depth proteomics analysis using high‐resolution data‐dependent analysis. Larvae reared at low pH were smaller than those reared at ambient pH, especially in the prodissoconch II phase of development, and displayed a delay in their competency for settlement. Proteomic profiles revealed that metabolic, cell cycle, and protein turnover pathways differed between the two pH and suggested that differing phenotypic outcomes between pH 7.5 and 7.1 are likely due to environmental disruptions to the timing of physiological events. In summary, ocean acidification results in elevated energetic demand on geoduck larvae, resulting in delayed development and disruptions to normal molecular developmental pathways, such as carbohydrate metabolism, cell growth, and protein synthesis.     

不同微生物大鼠腹腔注射模型尿液蛋白组学的比较

不同的微生物都可以引起腹腔感染,文中尝试利用尿液来区分不同的微生物感染。通过在大鼠腹腔内分别注射大肠杆菌、金黄色葡萄球菌和白色念球菌建立3种模型,收集感染后0、12、36、72 h的尿液,并使用液相色谱串联质谱技术 (LC-MS/MS) 对尿蛋白进行分析。与感染前相比,在大肠杆菌腹腔注射模型中共鉴定到69个差异蛋白,在金黄色葡萄球菌腹腔注射模型中共鉴定到31个差异蛋白,在白色念球菌腹腔注射模型中共鉴定到38个差异蛋白。结果表明,腹腔注射不同的微生物时尿蛋白质组不同,提示尿液可能对不同的腹腔感染有鉴别诊断的潜能。     

蛹虫草组学研究进展

作为虫草属的模式种,蛹虫草是目前虫草类真菌中研究和应用最为广泛的物种之一。随着基因组序列的公布,蛹虫草组学水平的研究近年来取得了明显的进展。本文从基因组、线粒体基因组、甲基化组、转录组、蛋白质组、代谢网络等角度对蛹虫草组学水平的研究现状进行综述,期望对进一步推动蛹虫草的深入研究提供帮助。     

线粒体蛋白质组及蛋白质量控制

线粒体是哺乳动物细胞内重要细胞器,不仅通过氧化磷酸化产生ATP为细胞提供能量,也参与调节钙离子稳态、活性氧(reactive oxygen species,ROS)的产生、细胞应激反应和细胞死亡等过程,其功能障碍不仅导致多种人类疾病的发生,而且也能降低动物卵母细胞质量和早期胚胎发育能力。大量证据表明,线粒体的功能依赖于线粒体蛋白质组完整性和稳态。基于此,该文综述了线粒体蛋白组、线粒体蛋白转运,聚焦蛋白酶、分子伴侣、线粒体囊泡、线粒体自噬和线粒体未折叠蛋白反应在帮助正确的蛋白质折叠,去除错误折叠或聚集的蛋白质和清除功能失调的线粒体方面的作用,为调控线粒体蛋白质量,从而维持线粒体健康、降低疾病发生提供理论依据。     

Urinary and plasma proteomics to discover biomarkers for diagnosing between diabetic nephropathy and minimal change nephrotic syndrome or membranous nephropathy

The choice of treatment for primary nephrotic syndrome depends on the pathologic type of the disorder. Renal biopsy is necessary for a definitive diagnosis, but it is burdensome for the patients, and can be avoided if tests could be performed using urine or plasma. In this study, we analyzed 100 urinary proteins, 141 plasma proteins, and 57 urine/plasma ratios in cases of diabetic nephropathy (DN; n = 11), minimal change nephrotic syndrome (MCNS; n = 14), and membranous nephropathy (MN; n = 23). We found that the combination of urinary retinol-binding protein 4 and SH3 domain-binding glutamic acid-rich-like protein 3 could distinguish between MCNS and DN, with an area under the curve (AUC) of 0.9740. On the other hand, a selectivity index (SI) based on serotransferrin and immunoglobulin G, which is often used in clinical practice, distinguished them with an AUC of 0.9091. Similarly, the combination of urinary afamin and complement C3 urine/plasma ratio could distinguish between MN and DN with an AUC of 0.9842, while SI distinguished them with an AUC of 0.8538. Evidently, the candidates identified in this study were superior to the SI method. Thus, the aim was to test these biomarkers for accurate diagnosis and to greatly reduce the burden on patients.     

微重力环境对大鼠血浆蛋白质谱的影响

目的:探讨模拟失重环境下大鼠血浆蛋白质组变化特征.方法:健康成年雄性 Wistar 大鼠88只,按模拟失重时相随机分为11组,分别为6 h、12 h、1 d、2 d、3 d、5 d、1周、2周、3周、4周及0 h 组(对照组).采用尾悬吊法建立模拟失重动物模型,实验结束时取动物静脉血,利用表面增强激光解吸电离飞行时间质谱(SELDI-TOF-MS)技术及 MB-WCX 磁珠检测大鼠静脉血浆蛋白质谱,应用 Ciphergen Protein Chip Software 3.2.0和 Biomarker Wizard 3.1.0软件分析数据.结果:发现18个重力敏感蛋白,其中在模拟失重早期,相对分子质量较小的6个蛋白的表达呈上调趋势,而相对分子质量较大的12个蛋白的表达则逐渐下调;在模拟失重后期(悬尾2~3周后),上述蛋白的表达均呈回归趋势.结论:模拟失重环境对大鼠静脉血浆蛋白质谱产生明显影响,研究重力敏感蛋白对进一步揭示失重对机体的影响及机制具有重要意义,并对医监医保可能有一定的价值.     

Inactivation of ntcA gene revealed differential proteome expression and induction of some hypothetical proteins in the cyanobacterium Anabaena sp. PCC 7120 and its derivative ntcA mutant under different levels of calcium

Abstract

Calcium is an important macronutrient for both prokaryotes and eukaryotes. It acts as an important second messenger mediating rapid response to environmental conditions. The present investigation deals with proteome profiling of Anabaena 7120 and its derivative ntcA mutant in response to varied calcium doses (0, 1 and 10?mM CaCl₂). Concentration of 1?mM CaCl₂ salt was the optimum concentration whereas 10?mM CaCl₂ was the inhibitory concentration for both the wild type and mutant strains. The results showed highly significant alteration in terms of protein abundance and differential response related to key processes of photosynthesis, energy and metabolism, nitrogen metabolism, oxidative and antioxidative defence, transport and signalling and fatty acid metabolism. In the wild type proteins related to photosynthesis and nitrogen metabolism showed upregulation at 1?mM CaCl₂ concentration while antioxidative defence related proteins were down-regulated. In the mutant however, proteins related to photosynthesis and nitrogen metabolism exhibited severe down-regulation. Some hypothetical proteins were also realized during proteome analysis. Overall, our results suggested that NtcA have a potential role in regulation of calcium ion dependent key processes underlying in various metabolic activities of the cyanobacterium Anabaena 7120.