Comparative Genomics Reveals 13 Different Isoforms of Mytimycins (A-M) in Mytilus galloprovincialis

Mytimycins are cysteine-rich antimicrobial peptides that show antifungal properties. These peptides are part of the immune network that constitutes the defense system of the Mediterranean mussel (Mytilus galloprovincialis). The immune system of mussels has been increasingly studied in the last decade due to its great efficiency, since these molluscs, particularly resistant to adverse conditions and pathogens, are present all over the world, being considered as an invasive species. The recent sequencing of the mussel genome has greatly simplified the genetic study of some of its immune genes. In the present work, we describe a total of 106 different mytimycin variants in 16 individual mussel genomes. The 13 highly supported mytimycin clusters (A–M) identified with phylogenetic inference were found to be subject to the presence/absence variation, a widespread phenomenon in mussels. We also identified a block of conserved residues evolving under purifying selection, which may indicate the “functional core” of the mature peptide, and a conserved set of 10 invariable plus 6 accessory cysteines which constitute a plastic disulfide array. Finally, we extended the taxonomic range of distribution of mytimycins among Mytilida, identifying novel sequences in M. coruscus, M. californianus, P. viridis, L. fortunei, M. philippinarum, M. modiolus, and P. purpuratus.     

Translesion Synthesis or Repair by Specialized DNA Polymerases Limits Excessive Genomic Instability upon Replication Stress

DNA can experience “replication stress”, an important source of genome instability, induced by various external or endogenous impediments that slow down or stall DNA synthesis. While genome instability is largely documented to favor both tumor formation and heterogeneity, as well as drug resistance, conversely, excessive instability appears to suppress tumorigenesis and is associated with improved prognosis. These findings support the view that karyotypic diversity, necessary to adapt to selective pressures, may be limited in tumors so as to reduce the risk of excessive instability. This review aims to highlight the contribution of specialized DNA polymerases in limiting extreme genetic instability by allowing DNA replication to occur even in the presence of DNA damage, to either avoid broken forks or favor their repair after collapse. These mechanisms and their key regulators Rad18 and Polθ not only offer diversity and evolutionary advantage by increasing mutagenic events, but also provide cancer cells with a way to escape anti-cancer therapies that target replication forks.     

Some Molecular and Cellular Stress Mechanisms Associated with Neurodegenerative Diseases and Atherosclerosis

Chronic stress is a combination of nonspecific adaptive reactions of the body to the influence of various adverse stress factors which disrupt its homeostasis, and it is also a corresponding state of the organism’s nervous system (or the body in general). We hypothesized that chronic stress may be one of the causes occurence of several molecular and cellular types of stress. We analyzed literary sources and considered most of these types of stress in our review article. We examined genes and mutations of nuclear and mitochondrial genomes and also molecular variants which lead to various types of stress. The end result of chronic stress can be metabolic disturbance in humans and animals, leading to accumulation of reactive oxygen species (ROS), oxidative stress, energy deficiency in cells (due to a decrease in ATP synthesis) and mitochondrial dysfunction. These changes can last for the lifetime and lead to severe pathologies, including neurodegenerative diseases and atherosclerosis. The analysis of literature allowed us to conclude that under the influence of chronic stress, metabolism in the human body can be disrupted, mutations of the mitochondrial and nuclear genome and dysfunction of cells and their compartments can occur. As a result of these processes, oxidative, genotoxic, and cellular stress can occur. Therefore, chronic stress can be one of the causes forthe occurrence and development of neurodegenerative diseases and atherosclerosis. In particular, chronic stress can play a large role in the occurrence and development of oxidative, genotoxic, and cellular types of stress.     

Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing

Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been developed to overcome this deficiency, which have not been benchmarked for genomic analyses of bacterial pathogens using Oxford Nanopore long reads. In this study, long-read assemblers, namely Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta, were thus benchmarked using Oxford Nanopore long reads of bacterial pathogens. Ten species were tested for mediocre- and low-quality simulated reads, and 10 species were tested for real reads. Raven was the most robust assembler, obtaining complete and accurate genomes. All Miniasm/Racon and Raven assemblies of mediocre-quality reads provided accurate antimicrobial resistance (AMR) profiles, while the Raven assembly of Klebsiella variicola with low-quality reads was the only assembly with an accurate AMR profile among all assemblers and species. All assemblers functioned well for predicting virulence genes using mediocre-quality and real reads, whereas only the Raven assemblies of low-quality reads had accurate numbers of virulence genes. Regarding multilocus sequence typing (MLST), Miniasm/Racon was the most effective assembler for mediocre-quality reads, while only the Raven assemblies of Escherichia coli O157:H7 and K. variicola with low-quality reads showed positive MLST results. Miniasm/Racon and Raven were the best performers for MLST using real reads. The Miniasm/Racon and Raven assemblies showed accurate phylogenetic inference. For the pan-genome analyses, Raven was the strongest assembler for simulated reads, whereas Miniasm/Racon and Raven performed the best for real reads. Overall, the most robust and accurate assembler was Raven, closely followed by Miniasm/Racon.     

Evolution of MicroRNA Biogenesis Genes in the Sterlet (Acipenser ruthenus) and Other Polyploid Vertebrates

MicroRNAs play a crucial role in eukaryotic gene regulation. For a long time, only little was known about microRNA-based gene regulatory mechanisms in polyploid animal genomes due to difficulties of polyploid genome assembly. However, in recent years, several polyploid genomes of fish, amphibian, and even invertebrate species have been sequenced and assembled. Here we investigated several key microRNA-associated genes in the recently sequenced sterlet (Acipenser ruthenus) genome, whose lineage has undergone a whole genome duplication around 180 MYA. We show that two paralogs of drosha, dgcr8, xpo1, and xpo5 as well as most ago genes have been retained after the acipenserid-specific whole genome duplication, while ago1 and ago3 genes have lost one paralog. While most diploid vertebrates possess only a single copy of dicer1, we strikingly found four paralogs of this gene in the sterlet genome, derived from a tandem segmental duplication that occurred prior to the last whole genome duplication. ago1,3,4 and exportins1,5 look to be prone to additional segment duplications producing up to four-five paralog copies in ray-finned fishes. We demonstrate for the first time exon microsatellite amplification in the acipenserid drosha2 gene, resulting in a highly variable protein product, which may indicate sub- or neofunctionalization. Paralogous copies of most microRNA metabolism genes exhibit different expression profiles in various tissues and remain functional despite the rediploidization process. Subfunctionalization of microRNA processing gene paralogs may be beneficial for different pathways of microRNA metabolism. Genetic variability of microRNA processing genes may represent a substrate for natural selection, and, by increasing genetic plasticity, could facilitate adaptations to changing environments.     

庆大霉素适应性菌株遗传稳定性研究

适应性进化是工业微生物遗传育种的重要技术手段之一。以庆大霉素连续进化1 200代的干酪乳杆菌Zhang为研究对象,将其在去掉选择压力的培养基中连续传1 000代,对其细胞形态、活菌数、浊度、耐药表型、基因型的变化进行跟踪监测。研究结果显示:适应性菌株在去掉选择压力环境中进化1 000代后,其细胞形态、活菌数、浊度及耐药表型趋于稳定;基因组仅检测到11个突变位点,包括4个同义突变位点和7个非同义突变位点。干酪乳杆菌Zhang庆大霉素适应性菌株具有良好的遗传稳定性。     

Silicon-containing fluorenylacetylene resins with low curing temperature and high thermal stability

Silicon-containing arylacetylene resins (PSAs) are promising thermal stability polymers for many applications. However, the controllability of curing reaction limited their application because of the high curing temperature and enthalpy. In this study, Materials Genome Initiative was utilized to screen out a target monomer, 2,7-diethynyl-9H-fluorene (DEF), for design of new PSAs with low curing temperature and enthalpy. After incorporation of DEF, the obtained silicon-containing fluorenylacetylene resins (PSA-VBF) could be cured at a lower temperature of 149.2 °C with lower enthalpy (239.8 J g⁻¹) than the reported PSA-V (190.0 °C, 368.3 J g⁻¹). Moreover, the thermal curing behavior and mechanism were investigated by differential scanning calorimetry, Fourier transform infrared, and pyrolysis-gas chromatography–mass spectrometry. The results revealed that with the increased of DEF, the curing reaction of PSA-VBF became dominated by Diels–Alder reaction. And the formed aromatic fused rings endowed the cured PSA-VBF with excellent thermal stability, which were proved by thermogravimetric analysis results that the temperature at 5% weight loss (T_d5) of the cured copolymers ranged from 630 to 639 °C, and the char yield at 1000 °C was above 90%. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019 , 136, 48262.     

食品中2株非常见耶尔森菌分离鉴定及耐药性分析

目的 对食品中两株Yersinia aleksiciae(Ya)进行分离鉴定及耐药性分析研究,为非常见耶尔森菌属菌株的分离鉴定提供技术储备。方法 2018年8月至2019年3月采集猪肉、牛肉、鸡肉食品样品,共300份。对分离到的疑似Ya菌株完成生化鉴定、耐药表型鉴定和全基因组测序分析。结果 食品样品中Ya的检出率为0.7%(2/300),生化鉴定中Ya与小肠结肠炎耶尔森菌(Yersinia enterocolitica,Ye)最大区别是Ye为赖氨酸脱羧酶阴性,Ya为赖氨酸脱羧酶阳性。Ya暂未发现与Ye类似的对氨苄西林、I代头孢菌素、替卡西林等抗生素的天然耐药性,两株Ya菌株的耐药性不同。全基因组测序比对16S rRNA和gyrB、rpoD基因三个片段序列,证实两株分离菌株为Ya。结论 分离到的两株Ya为国内首次发现,目前国外鲜有从食品中分离出该菌的报道。本研究提供的方法可用于其他非常见耶尔森菌的分离鉴定。