Selenocysteine tRNAs as Central Components of Selenoprotein Biosynthesis in Eukaryotes

Selenocysteine (Sec) tRNAs serve as carrier molecules for the biosynthesis of Sec from serine and to donate Sec to protein in response to specific UGA codons. In this study, we describe the current status of Sec tRNAs in higher animals and further we exarnine: (i) the Sec tRNA population in Drosophila; (ii) transcription of the Sec tRNA in vivo (in Xenopus oocytes) and in vitro (in Xenopus oocyte extracts); (iii) the effect of selenium on the Sec tRNA population in various rat tissues following replenishment of extremely selenium deficient rats with this element; and (iv) the biosynthesis of the modified bases on Sec tRNA in Xenopus oocytes

The ubiquity and coexistence of two FBPases in chloroplasts of photosynthetic eukaryotes and its evolutionary and functional implications

In photosynthetic eukaryotes,there are two well-characterized fructose-1,6-bisphosphatases(FBPases):the redox-insensitive cytosolic FBPase(cyFBPase),which participates in gluconeogenesis,and the redoxsensitive chloroplastic FBPase(cpFBPasel),which is a critical enzyme in the Calvin cycle.Recent studies have identified a new chloroplastic FBPase,cpFBPase2;however,its phylogenetic distribution,evolutionary origin,and physiological function remain unclear.In this study,we identified and characterized these three FBPase isoforms in diverse,representative photosynthetic lineages and analyzed their phylogeny.In contrast to previous hypotheses,we found that cpFBPase2 is ubiquitous in photo synthetic eukaryotes.Additionally,all cpFBPase2 s from diverse lineages form a monophyly,suggesting cpFBPase2 is not a recently evolved enzyme restricted to land plants but rather evolved early in the evolution of photo synthetic organisms,and most likely,in the common ancestor of photosynthetic eukaryotes.cyFBPase was probably first duplicated to produce cpFBPase2,and then the latter duplicated to produce cpFBPase1.The ubiquitous coexistence of these two cpFBPases in chloroplasts is most likely the consequence of adaptation to different redox conditions of photosynthesis,especially those caused by recurrent changes in light conditions.

Applications of genetic code expansion technology in eukaryotes

Unnatural amino acids(UAAs)have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins.In eukaryotes,genetic code expansion(GCE)enables the incorporation of UAAs and facilitates posttranscriptional modification(PTM),which is not feasible in prokaryotic systems.GCE is also a powerful tool for cell or animal imaging,the monitoring of protein interactions in target cells,drug development,and switch regulation.Therefore,there is keen interest in utilizing GCE in eukaryotic systems.This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.

Planktonic microbial eukaryotes in polar surface waters: recent advances in high-throughput sequencing

Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles.Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity,revealing a huge,previously underestimated phylogenetic diversity with many new lineages.This technology has now become the most important tool to understand the ecological signifcance of this huge and novel diversity in polar oceans.In particular,high-throughput sequencing technologies have been successfully applied to enumerate and compare marine microbial diversity in polar environments.Here,a brief overview of polar microbial eukaryote diversity,as revealed by in-situ surveys of the high-throughput sequencing on 18S rRNA gene,is presented.Using these‘omic’approaches,further attention still needs to be focused on diferences between specifc locations and/or entire polar oceans and on bipolar comparisons of diversity and distribution.

Archaea, the tree of life, and cellular evolution in eukaryotes

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the Archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered.

Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr-and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota,respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.

Effects of Biostimulation-Bioaugmentation on Coastal Microbial Community in an in situ Mesocosm System

Globally,various types of pollution affect coastal waters as a result of human activities.Bioaugmentation and biostimulation are effective methods for treating water pollution.However,few studies have explored the response of coastal prokaryotic and eukaryotic communities to bioaugmentation and biostimulation.Here,a 28-day outdoor mesocosm experiment with two treatments(bioaugmentation-A and combined treatment of bioaugmentation and biostimulation-AS)and a control(untreated-C)were carried out.The experiment was conducted in Meishan Bay to explore the composition,dynamics,and co-occurrence patterns of prokaryotic and eukaryotic communities in response to the A and AS using 16S rRNA and 18S rRNA gene amplicon sequencing.After treatment,Gammaproteobacteria and Epsilonproteobacteria were significantly increased in group AS compared to group C,while Flavobacteriia and Saprospirae were significantly reduced.Dinoflagellata was significantly reduced in AS compared to C,while Chrysophyta was significantly reduced in both AS and A.Compared to C,the principal response curve analyses of the prokaryotic and eukaryotic communities both showed an increasing trend followed by a decreasing trend for AS.Furthermore,the trends of prokaryotic and eukaryotic communities in group A were similar to those in group AS compared with group C,but AS changed them more than A did.According to the species weight table on principal response curves,a significant increase was observed in beneficial bacteria in prokaryotic communities,such as Rhodobacterales and Oceanospirillales,along with a decrease in autotrophs in eukaryotic communities,such as Chrysophyta and Diatom.Topological properties of network analysis reveal that A and AS complicate the interactions between the prokaryotic and eukaryotic communities.Overall,these findings expand our understanding of the response pattern of the bioaugmentation and biostimulation on coastal prokaryotic and eukaryotic communities.

Cloning and Expression Analysis of a Human Putative Tumor Suppressor Gene Homologue from Rice

A gene homologous to the human Putative tumor suppressor gone QM, designated OSQM1, was isolated from rice (Oryza sativa L.) genomic DNA library using through homology screening. It contained 4 exons and 3 introns, encoding a protein of 219 amino acids with 46 basic amino acids, leading to a high isoelectric point of 11.02. Homology search showed that this gene existed in eukaryotes and highly conserved throughout eukaryotes, suggesting an essential role of this gene. Northern Not analysis showed that it was expressed in various rice organs, but at lower level in developing flower and callus tissue than in other vegetative organs. Its expression levels in roots and leaves were influenced by different environmental factors.

The Construction and Identification of Eukaryotic Expression Vector pEGFP-N1-hTERT

[Objective] The aim of this study is to construct eukaryotic expression vector pEGFP-N1-hTERT and observe its expression in eukaryotic cells.[Method]The eukaryotic expression vector pEGFP-N1-hTERT was constructed with pC1-neo-hTERT and pEGFP-N1 plasmids,and the accuracy of human telomerase reverse transcriptase(hTERT)gene fragment was confirmed by double enzyme digestion and DNA sequencing analysis.After transfecting pEGFP-N1-hTERT into rat fetal neural stem cells(NSCs),the protein localization of human telomerase reverse transcriptase were indirectly observed through green fluorescent protein in the cells,and the correctness of constructed pEGFP-N1-hTERT was certificated by RT-PCR and Western Blot analysis.[Result]The eukaryotic expression vector pEGFP-N1-hTERT had correct structure and could express in eukaryotic cells.[Conclusion]This study laid a foundation for the establishment of immortalized NSCs line in rats.

食蟹猴疟原虫 (Plasmodium cynomolgi)中一个真核翻译起始因子4A(eIF-4A)同源蛋白的cDNA克隆、表达和ATP酶活性测定(英文)

真核翻译起始因子 4A(eukaryoticinitiationfactor 4A ,eIF 4A)是DEAD盒蛋白家族的ATP依赖性的RNA解旋酶类中的一个原型成员 .它在真核细胞的蛋白质合成的起始过程中起着关键性作用 .通过PCR扩增和放射探针杂交相结合的方法筛选食蟹猴疟原虫 (Plasmodiumcynomolgi)的cDNA文库 ,克隆了一个eIF 4A同源蛋白的完整cDNA序列 ,命名为CH1F .CH1F全长 1 75 3bp ,包含一个1 1 97bp的完整阅读框 ,推测编码一个由 398个氨基酸组成的蛋白 .对CH1F的蛋白序列用BlastP进行搜索和分析 ,提示它应该是DEAD盒家族的一个eIF 4A同源蛋白 ;用DNAStar将其与许多典型的DEAD盒蛋白序列进行比对分析 ,结果显示 :比起其它的DEAD盒蛋白 ,它与eIF 4A或eIF 4A的同源蛋白具有更高的同源性和更多序列上的相似结构域 .将包含完整阅读框的片段亚克隆进表达载体pET 2 8a (+) ,在大肠杆菌DH5α中表达 ,产生的融合蛋白大小在 4 5kD左右 .对该融合蛋白进行纯化、重新折叠和初步鉴定 .ATP酶活性检测显示 ,该融合蛋白只有很低的ATP酶活性 ,而且它的ATP酶活性似乎不依赖于核酸底物 .对这一检测结果给出 3种可能的原因 .这一检测结果与根据序列分析得到的推论———CH1F蛋白可能是一个eIF

Tissue cell differentiation and multicellular evolution via cytoskeletal stiffening in mechanically stressed microenvironments

Evolution of eukaryotes from simple cells to complex multicellular organisms remains a mystery. Our postulate is that cytoskeletal stiffening is a necessary condition for evolution of complex multicellular organisms from early simple eukaryotes. Recent findings show that embryonic stem cells are as soft as primitive eukaryotes-amoebae and that differentiated tissue cells can be two orders of magnitude stiffer than embryonic stem cells. Soft embryonic stem cells become stiff as they differentiate into tissue cells of the complex multicellular organisms to match their microenvironment stiffness. We perhaps see in differentiation of embryonic stem cells (derived from inner cell mass cells) the echo of those early evolutionary events. Early soft unicellular organisms might have evolved to stiffen their cytoskeleton to protect their structural integrity from external mechanical stresses while being able to maintain form, to change shape, and to move.

Construction and Preliminary Identification of Eukaryotic Expression Vector of Cryptosporidium parvum miR-2980

[Objective] This study aimed to construct and preliminarily identify the eu- karyotic expression vector of Cryptosporidium parvum miR-2980. [Method] The cp-miR- 2980 precursor was amplified from C. parvum genomic DNA and cloned into pMD18- T vector. The amplified precursor was then subcloned into pVAX I vector and identi- fied with restriction endonuclease digestion and sequencing. The recombinant plasmid pVAX-miR2980 was transfected into HCT-8 cells. Total RNA was extracted and the expression of cp-miR-2980 was evaluated by RT-PCR detection. [Result] The results showed that the recombinant eukaryotic expression vector pVAX-miR2980 was suc- cessfully constructed, which can express cp-miR-2980 in HCT-8 cell. [Conclusion] This study laid the foundation for further exploring the biological function of cp-miR-2980.

Construction of Eukaryotic Expression Vector with Partial Encoding Sequence of Actin from Cryptosporidium andersoni

[Objective] To clone the actin gene of Cryptosporidium andersoni, and to study its eukaryotic expression in Hela cells. [Methed] Specific primers were designed for the partial encoding sequence of actin, which were obtained by screening the T7 phage display library of Cryptosporidium andersoni, and the actin gene CA42 was amplified by PCR. Recombinant eukaryotic expression plasmid pVAX1-CA42 was constructed and transfected to Hela cells with lipofection strategy. Indirect im- munofluorescence staining, SDS-PAGE and Western blotting analysis were used to detect the expression of recombinant protein in Hela cells. [Result] CA42 protein was successfully expressed in Hela cells, and the expression products had reactogenicity. [Conclusion] The partial encoding sequence of actin from Cryptosporidium andersoni has been successfully cloned, and it can be stably expressed in Hela Cells

Establishment of BHK-21 Stable Cell Lines Expressing T7 RNAP and GFP

[Objective] The aim was to establish the BHK-21 stable cell lines expressing T7 RNAP and GFP.[Method]T7 RNAP gene was amplified from E.coli BL21（DE3）and inserted into FG12 vector.The lenti-virus recombinant plasmid FG12-T7 RNAP plasmid was obtained via identification with double enzymes digestion and gene sequencing.The transient expressed T7 RNAP protein was determined by WB in 293T cells transfected with FG12-T7 RNAP plasmid.The recombinant FG12-RNAP lenti-virus was packaged up by transfecting the 293 cells with the recombinant vector FG12-RNAP and the helper plasmids via lipofectamine-2000,which was then used to infect BHK-21 cells.The positive cell clones were obtained after continuous screening by GFP.The expression of T7 RNAP gene was confirmed by Western blot.[Result]The cell line stably expressing the T7 RNAP gene was established by Western blot.[Conclusion]T7 RNAP gene could be stably expressed in eukaryotic cells and it provided a good platform to rescue RNA virus in vivo.

Expression and Purification of Arabidopsis High Mobility Group B Protein Gene At2G34450 in Pichia pastoris

[Objective] The aim was to study the expression of Arabidopsis gene A/2G34450 in Pichia pastoris and to obtain recombinant Arabidopsis HMGB protein. [Method] The At2G34450 gene was cloned into yeast expression vector pPIC9K containing AOXl promoter and the sequences of secreting α-signal peptides. Recombinant plasmid was linearized by Sal l and transformed into P. pastoris GSl15 competent cells by electroporation. Positive integrated clones were screened out, and the At2G34450 protein was expressed under the induction of methanol. [Result] The At2G34450 protein was expressed in yeast medium through methanol induction. SDS-PAGE results showed that recombination product was At2G34450 protein. [Conclusion] At2G34450 protein was successfully expressed in the P. pastoris system for the first time, which paves a direct path to further research on the functions of HMGB family members.

The Prognostic Value of Pathological and Molecular Margins Marked by p53 and eIF4E in Laryngeal Carcinoma

Objective: To study the prognostic value of the pathological margin and molecular margin marked by eIF4E and P53 protein in laryngeal carcinoma. Methods: The prognostic value of pathological and molecular margin was studied in 253 cases and 67 cases respectively, the latter were pathological negative margin chosen from the former. Immunohistochemisty was used to detect the expression of eIF4E and p53 proteins. Results: The rate of pathological, p53 and eIF4E positive margins was 20.2%, 19.4% and 32.8% respectively. The recurrent rate of those with positive margins was higher than that of negative margins, which including pathological margin (70.6% vs 35.1%, P =0.0000), p53 margin (69.2% vs 33.3%, P =0.018) and eIF4E margin (63.6% vs 28.9%, P =0.018); The survival rate of those with negative margins was higher than those with positive margins, including pathological margin (the 5-year cumulative survival rate was 37.52% and 64.37% respectively, P =0.0023), p53 margin (the 5-year cumulative survival rate was 24.62% and 75.69% respectively, P =0.0012) and eIF4E margin (the 5-year cumulative survival rate was 43.31% and 77.52% respectively, P =0.0006). Conclusion: The prognosis of those with both pathological and molecular positive margins was worse than that of the negative margins; Both the eIF4E and p53 were useful markers to pick out the poor prognostic patients from those with pathological negative margin, and the former seemed to be more potential.

Construction of Eukaryotic Expression Vector for Pig Ghrelin Gene

[Objective] This study aimed to investigate the functions of transgenic growth related gene in pig growth. [Method] A pair of primers containing Nhe I and Hind Ⅲ restriction sites were designed by referring to the pig Ghrelin mRNA sequence published in Genbank. Total RNA was extracted from the small intestine tissue of 13/17 Robertson translocation heterozygous pig, and then was purified and used as the template in later RT-PCR reaction to amplify the full-length pig Ghrelin gene. The correct pig Ghrelin gene fragment was cloned into the pMD19-T simple vector for sequencing analysis. The obtained full-length cDNA of pig Ghrelin gene fragment was digested with both Nhe I and Hind Ⅲ, and then was linked into the eukaryotic expression vector pEGFP-N1 to obtain the recombinant plasmid pEGFPGhrelin. The recombinant plasmid was transected into the fibroblast cells to detect the fluorescence labeled gene expression. [Result] The nucleotide sequence extracted from 13/17 Robertson translocation heterozygous pig was the same as expected; and the eukaryotic expression vector pEGFP-Ghrelin was successfully constructed. [Conclusion] The eukaryotic expression vector constructed in this study can be further used in research on transgenic pigs, but also lays foundation for research on the regulatory mechanism of Ghrelin gene.

Distribution of Protists in the Deep South China Sea Revealed by High-Throughput Sequencing

Protists(microbial eukaryotes)are indispensable members of the marine microbial food web.In recent years,organisms living in the deep sea(>1000 m water depth)have increasingly become the focus of research;however,studies on protistan assemblages are relatively scarce compared with their prokaryotic counterparts.In the present study,high-throughput sequencing of the hypervariable V9 region of the 18S rRNA gene was used to explore the community composition of protists in bathypelagic waters of the South China Sea.Based on the analysis of the alpha and beta diversities of 14 samples,we discovered:1、members belonging to Rhizaria,Alveolata,and Excavata were the dominant groups in terms of both relative sequence abundance and operational taxonomic unit(OTU)richness in all samples,although their relative contributions differed among different samples;2、cluster analysis showed that the distribution of protistan assemblages was related neither to the sampling location nor to the water depth,and other environmental factors might have caused the differences among the communities;3、phototrophs,including members of the Bacillariophyta,Bolidophyceae,Dictyochophyceae,Prasinophyceae,and Prymnesiophyceae,were detected in all samples,which indicated their contributions to the downward transportation via the biological pump and the potential presence of phagotrophy of these phototrophic cells in the deep ocean.

Method for Tentative Evaluation of Membrane Permeability Coefficients for Sodium and Potassium Ions in Unicellular Organisms

The membrane permeability coefficient for sodium and potassium ions in unicellular organisms can be calculated using the data for cell volume, surface and mean generation time during growth and dividing of cells by binary. Accordingly theory of proposed method, the membrane permeability coefficients for passed trough outer cell membrane sodium and potassium ions, is equal to the volume of unicellular organism divided to product between cell surface and mean generation time of cells. The calculated by this way diapason of values overlaps with experimentally measured diapason of values of permeability coefficient for sodium and potassium ions. The deviation between the theoretically calculated and experimentally measured values of permeability coefficient does not exceed one order of magnitude.

Expanding-contracting Earth

The Earth was born from a giant impact at 4.56 Ga. It is generally thought that the Earth subsequently cooled, and hence shrunk, over geologic time. However, if the Earth＇s convection was double-layered, there must have been a peak of expansion during uni-directional cooling. We computed the expansion- contraction effect using first principles mineral physics data. The result shows a radius about 120 km larger than that of the present Earth immediately after the consolidation of the magma-ocean on the surface, and subsequent shrinkage of about 110 km in radius within about 10 m.y., followed by gradual expansion of 11 km in radius due to radiogenic heating in the lower mantle in spite of cooling in the upper mantle in the Archean. This was due to double-layered convection in the Archean with final collapse of overturn with contraction of about g km in radius, presumably by the end of the Archean. Since then, the Earth has gradually cooled down to reduce its radius by around 12 km. Geologic evidence supports the late Archean mantle overturn ca. 2.6 Ga, such as the global distribution of super-liqnidus flood basalts on nearly all cratonic fragments （〉35 examples）. If our inference is correct, the surface environment of the Earth must have undergone extensive volcanism and emergence of local landmasses, because of the thin ocean cover （3-5 km thickness）. Global unconformity appeared in cratonic fragments with stromatolite back to 2.9 Ga with a peak at 2.6 Ga. The global magmatism brought extensive crustal melting to yield explosive felsic volcanism to transport volcanic ash into the stratosphere during the catastrophic mantle overturn. This event seems to be recorded by sulfur mass-independent fractionation （SMIF） at 2.6 Ga. During the mantle overturn, a number of mantle plumes penetrated into the upper mantle and caused local upward doming of by ca. 2-3 km which raised local landmasses above sea-level. The consequent increase of atmospheric oxygen enabled life evolution from prokaryotes to eukaryotes by 2.1 Ga, or even earlier in the Earth history.