Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation

Background

Since the first fungal genome sequences became available, investigators have been employing comparative genomics to understand how fungi have evolved to occupy diverse ecological niches. The secretome, i.e. the entirety of all proteins secreted by an organism, is of particular importance, as by these proteins fungi acquire nutrients and communicate with their surroundings.

Results

It is generally assumed that fungi with similar nutritional lifestyles have similar secretome compositions. In this study, we test this hypothesis by annotating and comparing the soluble secretomes, defined as the sets of proteins containing classical signal peptides but lacking transmembrane domains of fungi representing a broad diversity of nutritional lifestyles. Secretome size correlates with phylogeny and to a lesser extent with lifestyle. Plant pathogens and saprophytes have larger secretomes than animal pathogens. Small secreted cysteine-rich proteins (SSCPs), which may comprise many effectors important for the interaction of plant pathogens with their hosts, are defined here to have a mature length of ≤ 300 aa residues, at least four cysteines, and a total cysteine content of ≥5%. SSCPs are found enriched in the secretomes of the Pezizomycotina and Basidiomycota in comparison to Saccharomycotina. Relative SSCP content is noticeably higher in plant pathogens than in animal pathogens, while saprophytes were in between and closer to plant pathogens. Expansions and contractions of gene families and in the number of occurrences of functional domains are largely lineage specific, e.g. contraction of glycoside hydrolases in Saccharomycotina, and are only weakly correlated with lifestyle. However, within a given lifestyle a few general trends exist, such as the expansion of secreted family M14 metallopeptidases and chitin-binding proteins in plant pathogenic Pezizomycotina.

Conclusions

While the secretomes of fungi with similar lifestyles share certain characteristics, the expansion and contraction of gene families is largely lineage specific, and not shared among all fungi of a given lifestyle.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-722) contains supplementary material, which is available to authorized users.     

Nutritionally rich marine proteins from fresh herring by-products for human consumption

Marine oils and proteins are valuable compounds, but under unfavorable conditions these components are easily oxidized and enzymatically degraded. We have designed an industrial process for producing high quality human grade proteins from fresh herring by-products. Two different processes were tested in semi-industrial scale: (i) thermal extraction to separate oil and proteins and (ii) enzymatic hydrolysis with different commercial proteases to produce fish protein hydrolysates (FPH) and separate oil. Both stick water from thermal extraction and fish protein hydrolysates, after hydrolysis, are nutritionally rich fractions and yielded approx. 18 and 25% of dry material in these fractions respectively. Neither season nor enzymes used influenced the color of hydrolysate powders, but time and temperature of the processes are important tools for controlling the color. Fishing seasons did not influence bitterness of hydrolysates and stick water samples, but both the process conditions and applied enzymes played an important role for the formation of bitterness. Insoluble fractions after both processes had significantly higher protein efficiency ratio: 3.08 and 2.93 compared to soluble fractions: 2.62 and 2.76 after hydrolysis and thermal extraction respectively. Both stick water and FPH showed antioxidative activity against both iron (15 μM of Fe³⁺) and hemoglobin (80 ppm) induced oxidation. Herring proteins (1.25 mg/ml) were able to reduce iron induced oxidation by 50–70%, while Hb induced oxidation was reduced by 70–80% using 4 mg/ml proteins concentration.     

三个褐飞虱寄主种群对氨基酸需求的分化(英文)

取分别在水稻品种TN1 (常用感虫对照 )、Mudgo(含Bph1 )或ASD7(含bph2 )上连续饲养 3 0代以上的3个褐飞虱Nilaparvatalugens寄主种群 ,分别饲养于 2 0种氨基酸总量与配比不同的全纯人工饲料上 ,以羽化率、短翅率、若虫历期以及初羽化成虫体重为指标对不同种群的氨基酸需求进行了比较。发现不同褐飞虱种群随氨基酸营养条件的改变有明显不同的表现 ,其中Mudgo种群最容易受到氨基酸营养条件的影响 ,而TN1种群所受影响最小。抗虫品种ASD7和Mudgo上的两褐飞虱种群所需的最佳氨基酸总浓度 (分别为 4 0 %～ 4 8%、4 0 % )高于TN1种群 (2 4%～ 3 2 % ) ,同时 ,前两种群对必需氨基酸浓度的变化较TN1种群敏感。这些结果表明 ,不同褐飞虱寄主种群对饲料氨基酸的需求存在明显的分化 ,推测氨基酸可能是抗虫水稻品种胁迫褐飞虱致害性变异的一种重要机制。     

环境因素与生姜需光特性关系研究

生姜光合作用的适宜光强与水分,温度及CO2等环境因素密切相关,80%的土壤相对含水量有利于生姜叶片利用较强的光照,其光合作用的饱和光强达1206μmol/m^-2.s^-1,水分胁迫可显著降低其对强光的适应性。40%土壤相对含水量时,光合作用的饱和光强权621μmol/L.m^-2.s^-1;而在正常供水条件下,以25-30℃的温度有利于生姜叶片对光能的利用;生姜对强光的适应能力随空气CO2浓度的升高而显著增强,CO2达1200μL/L时,其光合作用的饱和光强达1206μmol.m^-2.s^-1,但在220μL/L时,其光合作用的饱和光强仅608μumol.m^-2.s^-1。由此可以认为生姜应是喜光耐荫作物而非喜荫怕光作物,并据此偿试了以地面覆草取代传统插草栽培的可行性。     

Nucleic acid content as a potential growth rate estimator of Antarctic krill; results from field-caught krill from the indian sector of the southern ocean

Nucleic acid contents of tissue were determined from field-caught Antarctic krill to determine whether they could be used as an alternative estimator of individual growth rates which can currently only be obtained by labour intensive on-board incubations. Krill from contrasting growth regimes from early and late summer exhibited differences in RNA-based indices. There was a significant correlation between the independently measured individual growth rates and the RNA : DNA ratio and also the RNA concentration of krill tissue, although the strength of the relationship was only modest. DNA concentration, on average, was relatively constant, irrespective of the growth rates. The moult stage did not appear to have a significant effect on the nucleic acid contents of tissue. Overall, the amount of both nucleic acids varied considerably between individuals. Nucleic acid-based indicators may provide information concerning the recent growth and nutritional status of krill and further experimentation under controlled conditions is warranted. They are, however, reasonably costly and time-consuming measurements.     

Analysis of the growth performance,stress, profile of fatty acids and amino acids and cortisol in Tilapia (Oreochromis niloticus), cultured at high stocking density using in-pond raceway system

In-pond raceway system technology (IPRS) was introduced in Pakistan in 2019 as solution for sustainable aquaculture approach by effectively increasing production, reducing pollution and facilitating feed and pond management. Fingerlings of GIFT Tilapia (Oreochromis niloticus) (n = 16,500 in each raceway, initial weight = 32.00 ± 1.26 g) were stocked in June 2019 in two IPRS raceways (area of each raceway = 220 m³) for 171 days until harvested on November 30, 2019. Fingerlings stocked in traditional earthen ponds (area of each pond = 6167 m³) were studied as control (n = 3000 in each pond, initial weight = 32.00 ± 1.26 g). Average harvested biomass from raceways was 57.33 kg/m³ with an average daily weight gain per fish of 4.47 g per day. On the other hand, average harvested biomass from control ponds was 0.38 kg/m³ with an average daily weight gain per fish of 4.60 g per day. Average feed conversion ratio (FCR) in both raceways and control ponds was recorded as 1.25 and 1.24, respectively. Overall survival rate in both raceways and control ponds was above 99%. No sign of any disease was noted at any stage in both study groups. Crude protein and fats contents did not reduce in any raceway despite of high stocking density and sharp seasonal changes. Profile of essential and non-essential amino acids were found to be upto nutritional requirements of adult human. High levels of n-3 and n-6 fatty acids in fish collected from raceways as compared to those in traditional earthen pond show that muscle quality was not compromised due to high stocking density in small area. Return on investment excluding capital cost was 47.05 which implies that IPRS technology can be economically feasible with further modifications.     

The formation of flavonoids in cell suspension cultures ofPrunus x yedoensis matsum

Two lines of the red and pale yellow cell suspension cultures, prepared fromPrunus x yedoensis Matsum. callus induced by Murashige and Skoog's (1962) basal medium supplemented with 2, 4-dichlorophenoxyacetic acid (2, 4-D, 1.0 mg/l), kinetin (0.1 mg/l) and sucrose (30 g/l), were maintained on Schenk and Hildebrandt medium as modified by Mitchell and Gildow (1975). The red cell suspension culture produced cyanidin 3-monoglucoside, 5, 4′-dihydroxy-7-methoxyisoflavone 4′-glucoside (prunetrin), isoquercitrin, catechin, epicatechin, and procyanidin B-1, B-2, B-3 and B-4, while the pale yellow cells produced only a small amount of catechin and epicatechin as main flavonoids. These flavonoid compounds found in the red cell culture were present also in maturePrunus leaves. Maximum growth and maximum amount of total phenol and proanthocyanidin (procyanidins) were obtained with 0.3 mg/l of both 2,4-D and kinetin. Maximum concentration of anthocyanin was also obtained with 0.3 mg/l 2, 4-D regardless of kinetin concentration. Accumulation of proanthocyanidin was markedly stimulated by low concentrations of phosphate, which reduced growth by about half, and also by high concentrations of inorganic nitrogen. Production of both anthocyanin and proanthocyanidin was reduced by lowered nitrogen levels. Cell growth and production of all phenolics were inhibited when ammonium ion replaced nitrate in the medium.     

Vectors permitting visual monitoring of simple transposition events

The construction and use of two novel transposon(Tn)-delivery vectors is described. These vectors carry Inc.W or Inc.N broad-host-range transfer functions cloned next to the narrow-host-range replicon of pBR329. The host specificities of pSLX10 and pSLX23 both complement and extend the host specificities of existing Tn delivery vectors. Plasmids pSLX10 and pSLX23 were shown to transfer at high frequency in intergeneric matings. The lux genes which are present on each vector permit the visual monitoring of transconjugants which have retained a Tn element, but are devoid of plasmid molecules. pSLX10 and pLSX23 were efficiently used to generate a range of auxotrophic mutants in various strains of Pseudomonas as well as to clone genes from Serratia liquefaciens. These vectors may have general applicability to identify and clone genes in a wide range of Gram-negative bacteria.     

The effects of enriched CO2 atmospheres on plant-insect herbivore interactions: growth responses of larvae of the specialist butterfly,Junonia coenia (Lepidoptera: Nymphalidae)

Summary Little is known about the effects of enriched CO₂ environments, which are anticipated to exist in the next century, on natural plant-insect herbivore interactions. To begin to understand such effects on insect growth and survival, I reared both early and penultimate instar larvae of the buckeye, Junonia coenia (Lepidoptera: Nymphalidae), on leaves from one of their major hostplants, plantain, Plantago lanceolata (Plantaginaceae), grown in either ambient (350 PPM) or high (700 PPM) CO₂ atmospheres. Despite consuming more foliage, early instar larvae experienced reduced growth on high CO₂-grown compared to ambient CO₂-grown leaves. However, survivorship of early instar larvae was unaffected by the CO₂ treatment. Larval weight gain was positively correlated with the nitrogen concentration of the plant material and consumption was negatively correlated with foliar nitrogen concentration, whereas neither larval weight gain nor consumption were significantly correlated with foliar water or allelochemical concentrations. In contrast, penultimate instar larvae had similar growth rates on ambient and high CO₂-grown leaves. Significantly higher consumption rates on high CO₂-grown plants enabled penultimate instar larvae to obtain similar amounts of nitrogen in both treatments. These larvae grew at similar rates on foliage from the two CO₂ treatments, despite a reduced efficiency of conversion of ingested food (ECI) on the low nitrogen, high CO₂-grown plants. However, nitrogen utilization efficiencies (NUE) were unaffected by CO₂ treatment. Again, for late instar larvae, consumption rates were negatively correlated with foliar nitrogen concentrations, and ECI was also very highly correlated with leaf nitrogen; foliar water or allelochemical concentrations did not affect either of these parameters. Differences in growth responses of early and late instar larvae to lower nitrogen, high-CO₂ grown foliage may be due to the inability of early instar larvae to efficiently process the increased flow of food through the gut caused by additional consumption of high CO₂ foliage.