Different functional classes of genes are characterized by different compositional properties

A compositional analysis on a set of human genes classified in several functional classes was performed. We found out that the GC3, i.e. the GC level at the third codon positions, of the genes involved in cellular metabolism was significantly higher than those involved in information storage and processing. Analyses of human/Xenopus ortologous genes showed that: (i) the GC3 increment of the genes involved in cellular metabolism was significantly higher than those involved in information storage and processing; and (ii) a strong correlation between the GC3 and the corresponding GCi, i.e. the GC level of introns, was found in each functional class. The non-randomness of the GC increments favours the selective hypothesis of gene/genome evolution.     

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.     

Simulated long‐term effects of harvest and biomass residue removal on soil carbon and nitrogen content and productivity for two Upper Great Lakes forest ecosystems

We used the ecosystem process model Biome‐BGC to simulate the effects of harvest and residue removal management scenarios on soil carbon (C), available soil nitrogen (N), net primary production (NPP), and net ecosystem production (NEP) in jack pine (Pinus banksiana Lamb.) and sugar maple (Acer saccharum Marsh) ecosystems in northern Wisconsin, USA. To assess harvest effects, we simulated short (50‐year) and long (100‐year) harvest intervals, high (clear‐cut) and low (selective) harvest intensities, and three levels of residue retention (15%, 25%, and 35%) over a 500‐year period. The model simulation of NPP, soil C accumulation, and NEP agreed reasonably well with biometric and eddy‐covariance measurements of these two ecosystems. The more intensive (50‐year rotation clear‐cuts with low residue retention) harvest scenarios tended to have the greatest NEP (420 and 678 t C ha^?1 for the 500‐year interval for jack pine and sugar maple, respectively). All the harvest scenarios decreased mineral soil C and available mineral soil N content relative to the no‐harvest scenario for jack pine and sugar maple. The rate of change in mineral soil C decreased the greatest in the most intensive biomass removal scenarios (?0.012 and ?0.072 t C ha^?1 yr^?1 relative to no‐harvest for jack pine and sugar maple, respectively) and the smallest decrease was observed in the least intensive biomass removal scenarios (?0.002 and ?0.009 t C ha^?1 yr^?1 relative to no‐harvest for jack pine and sugar maple, respectively). The more intensive biomass removal harvest scenarios in sugar maple significantly decreased peak productivity (NPP) in the simulation period.     

Old and new glycopeptide antibiotics: From product to gene and back in the post-genomic era

Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics. We review the strategies adopted to increase microbial production (from classical strain improvement to rational genetic engineering), and the recent progress in genome mining, chemoenzymatic derivatization, and combinatorial biosynthesis for expanding glycopeptide chemical diversity and tackling the never-ceasing evolution of antibiotic resistance.     

草菇培养物中粗三萜和黄酮含量及抗氧化抗肿瘤活性研究

采用液体摇瓶法培养草菇菌丝体,并用不同有机溶剂对培养液及菌丝体中的代谢成分分别进行分离提取,获得了不同来源的次生代谢提取物。对各提取物的成分分析表明,石油醚相、乙酸乙酯相和乙醇相提取物中均含有粗三萜和黄酮类物质,但菌丝体提取物中粗三萜和黄酮含量明显高于培养液提取物中的含量。石油醚抽提菌丝体获得的提取物中粗三萜含量最高,达17%,而乙酸乙酯抽提菌丝体获得的提取物中黄酮含量最高,达9.31%。抗氧化活性检测结果显示,石油醚相、乙酸乙酯相、乙醇相中的代谢提取物均有较高的抗氧化活性,但乙酸乙酯相提取物的抗氧化活性明显高于石油醚相提取物,具最高抗氧化活性的提取物分别来自乙酸乙酯、乙醇对菌丝体的抽提物。MTT法检测各提取物对胃癌细胞增殖的抑制作用,结果显示各组分均有较高的抗肿瘤活性,且抗肿瘤活性与提取物浓度存在明显的量效关系。     

Hybrid Genome Assembly for Predicting Functional Potential of a Novel Streptomyces Strain as Plant Biomass Valorisation Agent

Environmental bioremediation relies heavily on the realized potential of efficient bioremediation agents or microbial strains of interest. Identifying suitable microbial agents for plant biomass waste valorization requires (i) high-quality genome assemblies to predict the full metabolic and functional potential, (ii) accurate mapping of lignocellulose metabolizing enzymes. However, fragmented nature of the sequenced genomes often limits the prediction ability due to breaks occurring in coding sequences. To address these challenges and as part of our ongoing agri-culturomics efforts, we have performed a hybrid genome assembly using Illumina and Nanopore reads with modified assembly protocol, for a novel Streptomyces strain isolated from the rhizosphere niche of green leafy vegetables grown in a commercial urban farm. High-quality genome was assembled with the size of 8.6 Mb in just two contigs with N50 of 8,542,030 and coverage of 383X. This facilitated identification and complete arrangement of approximately 248 CAZymes and 38 biosynthetic gene clusters in the genome. Multiple gene clusters consisting of cellulases and hemicellulases associated with substrate recognition domain were identified in the genome. Genes for lignin, chitin, and even some aromatic compounds degradation were found in the Streptomyces sp. genome which makes it a promising candidate for lignocellulosic waste valorization. Supplementary InformationThe online version contains supplementary material available at 10.1007/s12088-021-00935-5.     

草菇培养物中粗三萜和黄酮含量及抗氧化抗肿瘤活性研究

采用液体摇瓶法培养草菇菌丝体,并用不同有机溶剂对培养液及菌丝体中的代谢成分分别进行分离提取,获得了不同来源的次生代谢提取物。对各提取物的成分分析表明,石油醚相、乙酸乙酯相和乙醇相提取物中均含有粗三萜和黄酮类物质,但菌丝体提取物中粗三萜和黄酮含量明显高于培养液提取物中的含量。石油醚抽提菌丝体获得的提取物中粗三萜含量最高,达17%,而乙酸乙酯抽提菌丝体获得的提取物中黄酮含量最高,达9.31%。抗氧化活性检测结果显示,石油醚相、乙酸乙酯相、乙醇相中的代谢提取物均有较高的抗氧化活性,但乙酸乙酯相提取物的抗氧化活性明显高于石油醚相提取物,具最高抗氧化活性的提取物分别来自乙酸乙酯、乙醇对菌丝体的抽提物。MTT法检测各提取物对胃癌细胞增殖的抑制作用,结果显示各组分均有较高的抗肿瘤活性,且抗肿瘤活性与提取物浓度存在明显的量效关系。     

RNA干扰Chk1/2调控二烯丙基二硫诱导的G2/M期阻滞作用及相关周期蛋白表达

在细胞周期检测点信号传导通路中,Chkl和Chk2起着重要作用,主要参与G2/M期细胞周期检测点信号传导.首先采用RNAi技术在BGC823细胞中将Chk1、Chk2基因沉默,Chk1、Chk2 siRNA转染BGC823细胞后24h加入15mg/L二烯丙基二硫(diallyl disulfide,DADS),接着通过Real-timePCR、Western blot分析Chk1、Chk2基因在转染前后的表达差异,然后运用流式细胞术和Western blot分析Chk1、Chk2基因沉默后对DADS诱导的细胞周期G2/M期阻滞作用及相关周期蛋白CDC25C和cyclinB1表达的影响.实验结果表明,与未转染对照组相比,转染Chk1、Chk2siRNA后BGC823细胞中Chk1、Chk2表达明显被抑制,二者的mRNA表达分别下降84.7%和69.0%,蛋白质水平分别下降73.4%和78.5%.流式细胞术分析结果发现,ChklsiRNA转染的BGC823细胞在15mg/LDADS处理24h后,G2/M期比例由单纯DADS处理组的58.1%降至10.4%(P<0.05).但Chk2 siRNA转染后加入15mg/...     

Control of damping-off in tomato seedlings exerted by Serratia spp. strains and identification of inhibitory bacterial volatiles in vitro

Serratia marcescens can be a plant growth promoting bacteria (PGPB) and an opportunistic human and plant pathogen. We have identified and characterized strains of related species of Serratia and evaluated their biological control of damping-off of tomato seeds caused by Pythium cryptoirregulare. Serratia ureilytica, S. bockelmannii and S. nevei were identified by phylogenetic analysis of partial gyrB gene sequence and average nucleotide identity (ANI). Tomato seeds inoculated with S. ureilytica ILBB 145 showed higher germination percentage and reduced damping-off in greenhouse experiment resembling a commercial operation, and volatiles produced by this strain caused the nearly complete inhibition in vitro of P. cryptoirregulare. Analysis of volatile organic compounds (VOCs) showed that ILBB 145 produced dimethyl disulfide (DMDS), which can partially account for this inhibition. Serratia bockelmannii ILBB 162 performance against damping-off was intermediate and the inhibition of P. cryptoirregulare in vitro was lower and explained by volatile and diffusible metabolites. Both strains augmented DMDS production in the presence of P. cryptoirregulare, suggesting this compound may play a role in the context of interspecific competition. Serratia nevei ILBB 219 showed the lowest inhibition of P. cryptoirregulare in vitro, no DMDS production, and no biocontrol in planta. Draft genomes of the three strains were annotated and individual genes and biosynthesis gene clusters were identified in relation with the observed phenotypes. We report S. ureilytica – a low risk species- with activity as a biological control agent and DMDS produced by this bacterial species putatively involved in seed and seedling protection against P. cryptoirregulare.     

Vertebrate codon bias indicates a highly GC-rich ancestral genome

Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~ 60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~ 40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~ 65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences.