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1.
Evgenii A. Konorov Mikhail A. Nikitin Kirill V Mikhailov Sergey N. Lysenkov Mikhail Belenky Peter L. Chang Sergey V. Nuzhdin Victoria A. Scobeyeva 《BMC evolutionary biology》2017,17(1):39
Background
The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger – the most successful urban inhabitant of all ants – and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus.Results
Sequences from 272 M Illumina reads were assembled into 41,406 contigs with total length of 245 MB, and N50 of 16,382 bp, similar to other ant genome assemblies enabling comparative genomic analysis. Remarkably, the predicted proteome of L. niger is significantly enriched relative to other ant genomes in terms of abundance of domains involved in nucleic acid binding, DNA repair, and nucleotidyl transferase activity, reflecting transposable element proliferation and a likely genomic response. With respect to environmental stress, we note a proliferation of various detoxification genes, including glutatione-S-transferases and those in the cytochrome P450 families. Notably, the CYP9 family is highly expanded with 19 complete and 21 nearly complete members - over twice as many compared to other ants. This family exhibits the signatures of strong directional selection, with eleven positively selected positions in ligand-binding pockets of enzymes. Gene family contraction was detected for several components of the olfactory system, accompanied by instances of both directional selection and relaxation.Conclusions
Our results suggest that the success of L. niger in urbanized areas may be the result of fortuitous coincidence of several factors, including the expansion of the CYP9 cytochrome family due to coevolution with parasitic fungi, the diversification of DNA repair systems as an answer to proliferation of retroelements, and the reduction of olfactory system and behavioral preadaptations from non-territorial subdominant life strategies found in natural environments. Diversification of cytochromes and DNA repair systems along with reduced odorant communication are the basis of L. niger pollutant resistance and polyphagy, while non-territorial and mobilization strategies allows more efficient exploitation of large but patchy food sources.2.
Microorganisms that live in fluctuating environments must constantly adapt their behavior to survive. The host constitutes an important microenvironment in opportunistic and primary fungal pathogens like Cryptococcus neoformans (C. neoformans) and Cryptococcus gattii (C. gattii). In clonal populations, adaptation may be achieved through the generation of diversity. For fungi phenotype switching constitutes a mechanism that allows them to change rapidly. Both C. neoformans and C. gattii undergo phenotypic switching, which allows them to be successful pathogens and cause persistent disease. Similar to other encapsulated microbes that exhibit phenotypic variation, phenotypic switching in Cryptococcus changes the polysaccharide capsule. Most importantly, in animal models phenotypic switching affects virulence and can change the outcome of infection. Virulence changes because C. neoformans and C. gattii switch variants elicit different inflammatory responses in the host. This altered host response can also affect the response to antifungal therapy and in some cases may even promote the selection of switch variants. This review highlights the similarity and differences between phenotypic switching in C. neoformans and C. gattii, the two dominant species that cause cryptococcosis in humans. 相似文献
3.
Summary Direct observations have suggested that the closely related wood ants Formica polyctena and F. rufa represent different social organizations, with high queen number in F. polyctena and a high frequency of monogynous nests in F. rufa. We examined social organization and genetic population structure in a setup where populations of the two species are sympatric and gene flow between the species is possible. Our aim was to compare social organization in the species, and study evolutionary relationships between them. The observed relatedness among colony workers suggested that the difference in the level of polygyny is quantitative rather than qualitative, with a higher queen number in F. polyctena. The observed difference in polygyny was not accompanied by a difference in spatial genetic differentiation which was weak in both species. The genetic distance between the species is consistent with limited interspecific gene flow. Identification of a few possible F. rufa migrants in F. polyctena populations suggests potential interspecific gene flow. Thus, reproductive isolation of the species may not be complete when they are sympatric.Received 14 March 2003; revised 10 October 2003; accepted 20 October 2003. 相似文献
4.
Ae-Young Mo Bora Kwon Seralathan Kamala-Kannan Kui-Jae Lee Byung-Taek Oh Dae-Hyuk Kim Moon-Sik Yang Jin-Hyung Kim Seung-Moon Park 《World journal of microbiology & biotechnology》2010,26(6):1099-1105
Bacteria of the Bacillus species have been reported as an important microorganism in fermented soybean products. In the present study, thirty Bacillus isolates were screened from Meju, a Korean soybean fermentation starter. The comparative analysis of 16S rDNA sequences, 16S-23S internal transcribed spacer
sequences, phenotypic, and biochemical characterizations revealed three phylogenetically distinct groups namely Bacillus atrophaeus,
Bacillus polyfermenticus and Bacillus subtilis. The isolates were assayed for poly-γ-glutamate production and fibrinolytic activity. Among the isolates, B. polyfermenticus exhibited maximum poly-γ-glutamate production and fibrinolytic activity. Moreover, the soybean products fermented by B. polyfermenticus have increased the time taken for coagulation and hemorrhage in mice. The results of the present study clearly indicate the
functional role of B. polyfermenticus in fermented soybean products. 相似文献
5.
Susan Meijer Willem Adriaan de Jongh Lisbeth Olsson Jens Nielsen 《Applied microbiology and biotechnology》2009,84(1):157-167
The acuB gene of Aspergillus niger is an ortholog of facB in Aspergillus nidulans. Under carbon-repression conditions, facB is repressed, thereby preventing acetate metabolism when the repressing carbon source is present. Even though facB is reported to be repressed directly by CreA, it is believed that a basal level of FacB activity exists under glucose-repressive
conditions. In the present study, the effect of deletion of acuB on the physiology of A. niger was assessed. Differences in organic acid and acetate production, enzyme activities and extracellular amino and non-amino
organic acid production were determined under glucose-repressing and -derepressing conditions. Furthermore, consumption of
alternative carbon sources (e.g. xylose, citrate, lactate and succinate) was investigated. It was shown that AcuB has pleiotropic
effects on the physiology of A. niger. The results indicate that metabolic pathways that are not directly involved in acetate metabolism are influenced by acuB deletion. Clear differences in organic acid consumption and production were detected between the ∆acuB and reference strain. However, the hypothesis that AcuB is responsible for basal AcuA activity necessary for activation of
acetate metabolic pathways, even during growth on glucose, could not be confirmed. The experiments demonstrated that also
when acuB was deleted, no acetate was formed. Therefore, AcuB cannot be the only activator of AcuA, and another control mechanism has
to be available for activating AcuA. 相似文献
6.
K. Parvathi R. Naresh Kumar R. Nagendran 《World journal of microbiology & biotechnology》2007,23(5):671-676
Summary Biosorption of manganese from its aqueous solution using yeast biomass Saccharomyces cerevisiae and fungal biomass Aspergillus niger was carried out. Manganese biosorption equilibration time for A. niger and S. cerevisiae were found to be 60 and 20 min, with uptakes of 19.34 and 18.95 mg/g, respectively. Biosorption increased with rise in pH,
biomass, and manganese concentration. The biosorption equilibrium data fitted with the Freundlich isotherm model revealed
that A. niger was a better biosorbent of manganese than S. cerevisiae. 相似文献
7.
Imrich Turcovský Kristína Kuniková Hana Drahovská Eva Kaclíková 《Antonie van Leeuwenhoek》2011,99(2):257-269
The aim of this study was to identify and characterize Cronobacter spp. isolated from a range of foods. A total of 71 Cronobacter strains were isolated from 602 foods in our laboratory. The highest contamination was observed in foods of plant origin,
e.g. spices, teas, chocolate, nuts, pastries and vegetables. On the basis of genus and species identification performed using
genus-specific PCR, 16S rRNA sequencing and AFLP genotyping, most of the strains belonged to Cronobacter sakazakii. Biochemical profiling by the tests included in API 20E, complemented with relevant additional tests, classified the strains
into 13 biogroups. AFLP genotyping facilitated discrimination of six main groups at the 70% similarity level and strain grouping
correlated clearly with species identification. Our results indicate that molecular typing by AFLP may be applied as a useful
tool not only for direct comparison of Cronobacter isolates, providing traceability, but also for the reliable species classification. Moreover, tracing of these bacteria in
a wider variety of foods should be important to enhance the knowledge of their transmission. 相似文献
8.
Y. P. Vinetsky A. M. Rozhkova A. M. Chulkin A. D. Satrutdinov O. A. Sinitsyna E. A. Fedorova A. O. Bekkarevich O. N. Okunev A. P. Sinitsyn 《Biochemistry. Biokhimii?a》2009,74(8):882-887
The gene encoding the xlnR xylanolytic activator of the heterologous fungus Aspergillus niger was incorporated into the Penicillium canescens genome. Integration of the xlnR gene resulted in the increase in a number of activities, i.e. endoxylanase, β-xylosidase, α-L-arabinofuranosidase, α-galactosidase, and feruloyl esterase, compared to the host P. canescens PCA 10 strain, while β-galactosidase, β-glucosidase, endoglucanase, and CMCase activities remained constant. Two different expression constructs were developed. The first consisted of the nucleotide sequence containing the mature P. canescens phytase gene under control of the axhA promoter region gene encoding A. niger (1,4)-β-D-arabinoxylan-arabinofuranohydrolase. The second construct combined the P. canescens phytase gene and the bgaS promoter region encoding homologous β-galactosidase. Both expression cassettes were transformed into P. canescens host strain containing xlnR. Phytase synthesis was observed only for strains with the bgaS promoter on arabinose-containing culture media. In conclusion, the bgaS and axhA promoters were regulated by different inducers and activators in the P. canescens strain containing a structural tandem of the axhA promoter and the gene of the xlnR xylanolytic activator. 相似文献
9.
Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes. 相似文献
10.
The ants Formica aquilonia and F. lugubris which inhabit the entire forest zone of the North Palaearctic and are absent from the basins of the Yana, Indigirka, and Kolyma rivers were found in the coastal area of the Sea of Okhotsk. A possible climatic conditionality of their occurrence in the Northeast is considered based on the data on the biotopic distribution of ants, the temperature causation of their overwintering, and cold hardiness. On the Sea of Okhotsk coast, these ants overwinter at a depth of 40–200 cm in the soil. During winter, the minimum soil temperature at a depth of 40 cm under the anthill was ?5°C. The supercooling temperature of F. aquilonia was not lower than ?20.2 ± 0.5°C, that of F. lugubris, not lower than ?19.6 ± 0.4°C. Half of F. aquilonia individuals did not survive the daily exposure at ?13°C, F. lugubris, at ?16°C. These two cold-resistant species could inhabit some biotopes of the Kolyma River basin, similar to F. exsecta, F. lemani, and F. sanguinea, but they are absent there for some reasons that are not related to the temperature. A similar cold hardiness is characteristic of F. aquilonia in Estonia (Maavara, 1971, 1985), where it represents a side effect of diapause, since excessive cold hardiness has no adaptive significance for insects overwintering in the non-freezing soils of Estonia. Colonization of Siberia by ant species turned out to be possible only due to the existing cold hardiness, i.e. preadaptation to low temperature. On the Sea of Okhotsk coast, cold hardiness of the ants is non-adaptive due to the relatively mild conditions during winter. 相似文献
11.
Fatemeh Khadivi Derakshan Farshad Darvishi Mehrouz Dezfulian Catherine Madzak 《Molecular biotechnology》2017,59(8):307-314
Glucose oxidase (GOX) is currently used in clinical, pharmaceutical, food and chemical industries. The aim of this study was expression and characterization of Aspergillus niger glucose oxidase gene in the yeast Yarrowia lipolytica. For the first time, the GOX gene of A. niger was successfully expressed in Y. lipolytica using a mono-integrative vector containing strong hybrid promoter and secretion signal. The highest total glucose oxidase activity was 370 U/L after 7 days of cultivation. An innovative method was used to cell wall disruption in current study, and it could be recommended to use for efficiently cell wall disruption of Y. lipolytica. Optimum pH and temperature for recombinant GOX activity were 5.5 and 37 °C, respectively. A single band with a molecular weight of 80 kDa similar to the native and pure form of A. niger GOX was observed for the recombinant GOX in SDS-PAGE analysis. Y. lipolytica is a suitable and efficient eukaryotic expression system to production of recombinant GOX in compered with other yeast expression systems and could be used to production of pure form of GOX for industrial applications. 相似文献
12.
In vitro colonization of hydrophilic contact lenses by Aspergillus niger was investigated. Five strains of the fungus, four polymers, two culture media and four incubation periods were considered
for analysis. Only the 2700 strain colonized the lenses. The degrees of adhesion and invasion varied significantly according
to the characteristics of the culture under investigation. Journal of Industrial Microbiology & Biotechnology (2002) 29, 6–9 doi:10.1038/sj.jim.7000255
Received 06 August 2001/ Accepted in revised form 23 March 2002 相似文献
13.
Two new effective microbial producers of inulinases were isolated from Jerusalem artichoke tubers grown in Thailand and identified
as Aspergillus niger TISTR 3570 and Candida
guilliermondii TISTR 5844. The inulinases produced by both these microorganisms were appropriate for hydrolysing inulin to fructose as the
principal product. An initial inulin concentration of ∼100 g l−1 and the enzyme concentration of 0.2 U g−1 of substrate, yielded 37.5 g l−1 of fructose in 20 h at 40°C when A. niger TISTR 3570 inulinase was the biocatalyst. The yield of fructose on inulin was 0.39 g g−1. Under identical conditions, the yeast inulinase afforded 35.3 g l−1 of fructose in 25 h. The fructose yield was 0.35 g g−1 of substrate. The fructose productivities were 1.9 g l−1 h−1 and 1.4 g l−1 h−1 for the mold and yeast enzymes, respectively. After 20 h of reaction, the mold enzyme hydrolysate contained 53% fructose
and more than 41% of initial inulin had been hydrolysed. Using the yeast enzymes, the hydrolysate contained nearly 38% fructose
at 25 h and nearly 36% of initial inulin had been hydrolysed. The A. niger TISTR 3570 inulinases exhibited both endo-inulinase and exo-inulinase activities. In contrast, the yeast inulinases displayed
mainly exo-inulinase activity. The mold and yeast crude inulinases mixed in the activity ratio of 5:1 proved superior to individual
crude inulinases in hydrolysing inulin to fructose. The enzyme mixture provided a better combination of endo- and exo-inulinase
activities than did the crude extracts of either the mold or the yeast individually. 相似文献
14.
Noel H. Holmgren 《Brittonia》2018,70(1):115-139
A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations. 相似文献
15.
Jian-Xia Zhang Kun-Lin Wu Li-Ning Tian Song-Jun Zeng Jun Duan 《Acta Physiologiae Plantarum》2011,33(2):409-417
16.
A genetic transformation system has been developed for callus cells of Crataegus
aronia using Agrobacterium
tumefaciens. Callus culture was established from internodal stem segments incubated on Murashige and Skoog (MS) medium supplemented with
5 mg l−1 Indole-3-butyric acid (IBA) and 0.5 mg l−1 6-benzyladenine (BA). In order to optimize the callus culture system with respect to callus growth and coloration, different
types and concentrations of plant growth regulators were tested. Results indicated that the best average fresh weight of red
colored callus was obtained on MS medium supplemented with 2 mg l−1 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.5 mg l−1 kinetin (Kin) (callus maintenance medium). Callus cells were co-cultivated with Agrobacterium harboring the binary plasmid pCAMBIA1302 carrying the mgfp5 and hygromycin phosphotransferase (hptII) genes conferring green fluorescent protein (GFP) activity and hygromycin resistance, respectively. Putative transgenic calli
were obtained 4 weeks after incubation of the co-cultivated explants onto maintenance medium supplemented with 50 mg l−1 hygromycin. Molecular analysis confirmed the integration of the transgenes in transformed callus. To our knowledge, this
is the first time to report an Agrobacterium-mediated transformation system in Crataegus
aronia. 相似文献
17.
Cytochrome c
6
, (cyt c
6) a soluble monoheme electron transport protein, was isolated and characterized from the chlorophyll d-containing cyanobacterium Acaryochoris marina, the type strain MBIC11017. The protein was purified using ammonium sulfate precipitation, ion exchange and gel filtration
column chromatography, and fast performance liquid chromatography. Its molecular mass and pI have been determined to be 8.87 kDa
and less than 4.2, respectively, by mass spectrometry and isoelectrofocusing (IEF). The protein has an alpha helical structure
as indicated by CD (circular dichroism) spectroscopy and a reduction midpoint potential (E
m) of +327 mV versus the normal hydrogen electrode (NHE) as determined by redox potentiometry. Its potential role in electron
transfer processes is discussed. 相似文献
18.
D. N. Goryunov 《Entomological Review》2015,95(8):953-958
Representatives of the subgenus Coptoformica build composite aboveground nests in much the same manner as red wood ants do. However, despite the superficial similarity, Coptoformica nests show a number of substantial differences that impact on the way in which ants use the nest. The aboveground part of a Formica (Coptoformica) exsecta nest consists of the temporary layer, the outer crust layer, the mound, and the intermediate layer. The material of all the layers includes soil and fragments of plants (picked up or excised), the relative proportion of the two components differing among the layers. The thick, soil-rich crust layer acts as armature and allows a variety of anthill shapes. The intermediate layer and the upper part of the mound harbor quite a few large chambers. Building material is often transferred from nest to nest. On the whole, F. exsecta nests are plastic and movable, which facilitates the activity of these ants in ecotone biotopes. 相似文献
19.
Studying Pneumocystis has proven to be a challenge from the perspective of propagating a significant amount of the pathogen in a facile manner.
The study of several fungal pathogens has been aided by the use of invertebrate model hosts. Our efforts to infect the invertebrate
larvae Galleria
mellonella with Pneumocystis proved futile since P. murina neither caused disease nor was able to proliferate within G. mellonella. It did, however, show that the pathogen could be rapidly cleared from the host. 相似文献