The chromosomal position of each centromere is determined epigenetically and is highly stable, whereas incremental cases have supported the occurrence of centromere repositioning on an evolutionary ...time scale (evolutionary new centromeres, ENCs), which is thought to be important in speciation. The mechanisms underlying the high stability of centromeres and its functional significance largely remain an enigma. Here, in the fission yeast Schizosaccharomyces pombe, we identify a feedback mechanism: The kinetochore, whose assembly is guided by the centromere, in turn, enforces centromere stability. Upon going through meiosis, specific inner kinetochore mutations induce centromere repositioning—inactivation of the original centromere and formation of a new centromere elsewhere—in 1 of the 3 chromosomes at random. Repositioned centromeres reside asymmetrically in the pericentromeric regions and cells carrying them are competent in mitosis and homozygotic meiosis. However, when cells carrying a repositioned centromere are crossed with those carrying the original centromere, the progeny suffer severe lethality due to defects in meiotic chromosome segregation. Thus, repositioned centromeres constitute a reproductive barrier that could initiate genetic divergence between 2 populations with mismatched centromeres, documenting a functional role of ENCs in speciation. Surprisingly, homozygotic repositioned centromeres tend to undergo meiosis in an inverted order—that is, sister chromatids segregate first, and homologous chromosomes separate second—whereas the original centromeres on other chromosomes in the same cell undergo meiosis in the canonical order, revealing hidden flexibility in the perceived rigid process of meiosis.
The scientific name of the traditional Chinese medicinal fungus, Sanghuang, has been clarified and confirmed that it is a new species -Sanghuangporus sanghuang in the recently discovered genus, ...Sanghuangporus. To maximize the yield of the active ingredients such as the triterpenoids from authentic Sanghuangporus sanghuang, four parameters of the extraction process, including the extraction time, solid-liquid ratio, extraction temperature, and ethanol concentration were determined. The Box-Behnken experimental design and the response surface method were used to optimize the triterpenoid extraction processes of Sanghuangporus sanghuang mycelium. The results showed that the parameters of the triterpenoid extraction processes were not simple linear relationships. Optimum conditions of ultrasonic extraction required an 80% ethanol concentration, a 1:20 solid-liquid ratio, a 20-min extraction time, and a 60 °C extraction temperature, to obtain a maximum triterpenoid extraction of 13.30 mg/g. Antioxidant capacity tests showed that the Sanghuangporus sanghuang triterpenoids had high clearance capabilities for hydroxyl free radicals, superoxide anions, 2,2-diphenyl-1-picrylhydrazyl free radicals, and 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonate) radicals, indicating that the Sanghuangporus sanghuang triterpenoids had high antioxidant activities.
Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, ...we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes,
,
,
,
,
,
,
,
,
,
, and
, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.
Recent developments in next-generation sequencing have enabled whole-genome profiling of nucleosome organizations. Although several algorithms for inferring nucleosome position from a single ...experimental condition have been available, it remains a challenge to accurately define dynamic nucleosomes associated with environmental changes. Here, we report a comprehensive bioinformatics pipeline, DANPOS, explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. Using both simulated and real nucleosome data, we demonstrated that bias correction in preliminary data processing and optimal statistical testing significantly enhances the functional interpretation of dynamic nucleosomes. The single-nucleotide resolution analysis of DANPOS allows us to detect all three categories of nucleosome dynamics, such as position shift, fuzziness change, and occupancy change, using a uniform statistical framework. Pathway analysis indicates that each category is involved in distinct biological functions. We also analyzed the influence of sequencing depth and suggest that even 200-fold coverage is probably not enough to identify all the dynamic nucleosomes. Finally, based on nucleosome data from the human hematopoietic stem cells (HSCs) and mouse embryonic stem cells (ESCs), we demonstrated that DANPOS is also robust in defining functional dynamic nucleosomes, not only in promoters, but also in distal regulatory regions in the mammalian genome.
The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity-nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, ...in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed "fragile nucleosomes" throughout the yeast genome, nearly 1000 of which were at previously determined "nucleosome-free" loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation, and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.
Plant endophytic bacteria play important roles in plants’ growth and resistance to stress. It is important to characterize endophytic bacteria to be able to understand their benefits. Matrix-assisted ...laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has become a powerful technique for bacterial identification due to its high throughput and simple procedures. In this study, the endophytic bacteria separated from Populus (the leaves, roots and stems of Populus tomentosa Carrière; stems of Populus nigra Linn. var. nigra; and stems of Populus canadensis Moench) were identified and classified based on MALDI-TOF MS data and 16S rRNA gene sequencing. The sampling and preparation of bacteria were optimized to obtain meaningful protein mass fingerprints. The composite correlation index (CCI) values of the inter-genera and inter-species protein mass fingerprints demonstrated sufficient differences between the strains. In the CCI value matrix for ten species in the same genus, all the CCI values were less than 0.5. Among the species, 95.6% of all the CCI values were less than 0.5. After data processing, the classification capacity of the protein mass fingerprints was verified using inter-specific and inter-generic PCoA. To compare different methods’ potential for differentiation and phylogenetic analysis, a dendrogram of the MS profiles and a phylogenetic tree based on the 16S rRNA gene sequences were constructed using 61 endophytic bacteria found in Populus. The clustering and grouping results show that the phylogenetic analysis based on MALDI-TOF MS is similar to that based on 16S rRNA gene sequencing. This study provides a valuable reference for differentiating and identifying endophytic bacteria according to their protein mass fingerprints.
•The fourth generation coupled platform of mass spectrometry (MS) is described.•The recent applications of chip-MS in proteomics and cell analysis are reviewed.•Chip-MS is an emerging platform for ...biological analysis.
Microchip-mass spectrometry (chip-MS) has been emerging as an excellent analytical tool in the analysis of complex biological samples. The microchip can play an important role, as in cell culture and sample-preparation steps prior to mass spectral identification, which benefit from its ability to handle small sample quantities with the potential for high-throughput parallel analysis. We describe recent progress in chip-MS, including approaches that combined microchip devices with electrospray ionization and matrix-assisted laser desorption/ionization. We then review the main applications of chip-MS in proteomics and cell analysis in the past three years. We also look at the implications for the future of the field.
Strain XMGL2
T
, isolated from rhizosphere soil of
Quercus mongolica
in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and ...rod-shaped. Growth occurred at 20–37 °C (optimum, 28 °C), pH 5.0–10.0 (optimum, pH 6.0), and with 0–1% NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XMGL2
T
was related to members of the genus
Sphingomonas
and had the highest 16S rRNA gene sequence identity to
Sphingomonas oleivorans
FW-11
T
(96.4%). The average nucleotide identity and digital DNA–DNA hybridization values between strain XMGL2
T
and the closely related taxa
Sphingomonas oleivorans
FW-11
T
and
Sphingomonas fennica
K101
T
were 75.3/19.8% and 75.8/20.2%, respectively. The major cellular fatty acids were C
18:1
ω
7
c
, C
14:0
2-OH, and C
16:0
. The major isoprenoid quinone was Q-10 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid and an unidentified phospholipid. The genomic DNA G + C content was 67.9%. Based on the phenotypic and genotypic properties and phylogenetic inference, strain XMGL2
T
represents a novel species of the genus
Sphingomonas
, for which the name
Sphingomonas quercus
sp. nov. is proposed. The type strain is XMGL2
T
(= JCM 34441
T
= GDMCC 1.2153
T
).
Poplar is a tree species with important production and application value. The symbiotic relationship between poplar and arbuscular mycorrhizal fungi (AMF) has a key role in ecosystem functioning. ...However, there remain questions concerning the seasonal dynamics of the AMF community in poplar roots, the relationship between AMF and the soil environment, and its ecological function.
Poplar roots and rhizosphere soil were sampled at the end of April and the end of October. The responses of AMF communities to season, host age, and host species were investigated; the soil environmental factors driving community changes were analyzed.
The diversity and species composition of the AMF community were higher in autumn than in spring. Season, host age, host species, and soil environmental factors affected the formation of the symbiotic mycorrhizal system and the AMF community. Differences in the communities could be explained by soil pH, total nitrogen, total phosphorus, total potassium, available potassium, and glomalin content.
The AMF community was sensitive to changes in soil physicochemical properties caused by seasonal dynamics, particularly total potassium. The change in the mycorrhizal symbiotic system was closely related to the growth and development of poplar trees.
Deadenylation is the major step triggering mammalian mRNA decay. One consequence of deadenylation is the formation of nontranslatable messenger RNA (mRNA) protein complexes (messenger ...ribonucleo-proteins mRNPs). Nontranslatable mRNPs may accumulate in P-bodies, which contain factors involved in translation repression, decapping, and 5′-to-3′ degradation. We demonstrate that deadenylation is required for mammalian P-body formation and mRNA decay. We identify Pan2, Pan3, and Caf1 deadenylases as new P-body components and show that Pan3 helps recruit Pan2, Ccr4, and Caf1 to P-bodies. Pan3 knockdown causes a reduction of P-bodies and has differential effects on mRNA decay. Knocking down Caf1 or overexpressing a Caf1 catalytically inactive mutant impairs deadenylation and mRNA decay. P-bodies are not detected when deadenylation is blocked and are restored when the blockage is released. When deadenylation is impaired, P-body formation is not restorable, even when mRNAs exit the translating pool. These results support a dynamic interplay among deadenylation, mRNP remodeling, and P-body formation in selective decay of mammalian mRNA.
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