Plasmid最新文献 - Book学术

Comparative genomics of diverse Escherichia coli O157:H7 strains to characterize plasmids, prophages, virulence and antimicrobial resistance genes 不同大肠杆菌O157:H7菌株的比较基因组学特征质粒、噬菌体、毒力和抗菌素耐药基因。

IF 2.2 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-12-08 DOI: 10.1016/j.plasmid.2025.102771

Sydney Menzeko Gambushe , Peter Ayodeji Idowu , Oliver Tendayi Zishiri

Plasmids play a critical role in bacterial evolution and represent major drivers of the emergence and dissemination of antimicrobial resistance. As primary mobile genetic elements (MGEs), plasmids facilitate the horizontal transfer of resistance determinants alongside genes associated with virulence, metabolic functions, and broader adaptive advantages. Recent studies have further highlighted the importance of conjugative plasmids, such as IncI1-like elements, in mediating the spread of extended-spectrum β-lactamase (ESBL) genes and other clinically relevant traits across diverse bacterial populations. Whether the recurrent detection of these plasmids is coincidental or reflects unique genetic features that enhance their capacity for transmission remains an important question in microbial genomics. In this context, the present study analyses complete genome sequences and whole-genome maps of Escherichia coli O157:H7 strains to characterize their antimicrobial resistance genes, virulence-associated loci, prophage content, and plasmid profiles. Publicly available sequences from the NCBI GenBank repository were examined using comparative genomic tools, including BRIG, VirulenceFinder, ResFinder, PlasmidFinder, and PHASTEST. This work also underscores the limited availability of whole-genome data for E. coli O157:H7 and O157:H7NM in developing regions, particularly within African countries, highlighting the need for expanded genomic surveillance. Comparative analyses revealed that most strains displayed high genomic similarity to the reference Sakai strain, with relatively few missing regions, although a subset exhibited reduced homology marked by numerous gaps. Prophages, bacteriophages integrated into the bacterial genome, were found to contribute substantially to genomic diversity, influencing virulence potential, antimicrobial resistance, and patterns of horizontal gene transfer. These findings emphasize the complex role of mobile genetic elements in shaping the evolution of E. coli O157:H7 and reinforce the importance of continued genomic sequencing to further elucidate the pathogen's diversity and adaptive mechanisms.

质粒在细菌进化中起着关键作用，是抗菌素耐药性出现和传播的主要驱动因素。作为主要的移动遗传元件（MGEs），质粒促进抗性决定因素与毒力、代谢功能和更广泛的适应优势相关基因的水平转移。最近的研究进一步强调了共轭质粒（如inci1样元件）在介导广谱β-内酰胺酶（ESBL）基因和其他临床相关性状在不同细菌群体中的传播中的重要性。这些质粒的反复检测是巧合还是反映了增强其传播能力的独特遗传特征，仍然是微生物基因组学中的一个重要问题。在此背景下，本研究分析了大肠杆菌O157:H7菌株的全基因组序列和全基因组图谱，以表征其抗微生物药物抗性基因、毒力相关位点、噬菌体含量和质粒谱。使用比较基因组工具（包括BRIG、VirulenceFinder、ResFinder、PlasmidFinder和PHASTEST）检查NCBI GenBank库中公开可用的序列。这项工作还强调了在发展中地区，特别是在非洲国家，O157:H7和O157:H7NM大肠杆菌全基因组数据的可得性有限，突出了扩大基因组监测的必要性。比较分析显示，大多数菌株与参考Sakai菌株具有较高的基因组相似性，缺失区域相对较少，尽管一个子集表现出同源性降低，标记为许多空白。原噬菌体是整合到细菌基因组中的噬菌体，被发现对基因组多样性做出了重大贡献，影响了毒力潜力、抗菌素耐药性和水平基因转移模式。这些发现强调了移动遗传元件在塑造大肠杆菌O157:H7进化过程中的复杂作用，并强调了继续进行基因组测序以进一步阐明病原体多样性和适应机制的重要性。

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引用次数: 0

Megaplasmids of the enteropathogenic species Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus represent a group of novel genetic elements unrelated to other plasmids of Vibrionaceae 肠致病性物种副溶血性弧菌、霍乱弧菌和创伤弧菌的巨型质粒代表了一组与其他弧菌科质粒无关的新遗传元件

IF 2.2 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-12-06 DOI: 10.1016/j.plasmid.2025.102770

Maria Borowiak, Jens A. Hammerl, Eckhard Strauch

Vibrio (V.) parahaemolyticus is a marine-associated bacterium that has previously been linked to foodborne illness associated with seafood consumption. Various plasmids harbouring antimicrobial resistance and virulence genes have been described for V. parahaemolyticus. By whole genome sequencing, we found two V. parahaemolyticus strains harbouring a large additional circular genomic element of 0.882 Mbp. NCBI database search revealed that this element represents a rare but globally distributed megaplasmid detected in four additional Vibrio strains spanning distinct species (V. parahaemolyticus, V. cholerae and V. vulnificus), geographical origins, and hosts. In addition to the two megaplasmid-harbouring V. parahaemolyticus strains from our study, we also identified two megaplasmid-free isogenic strains in our strain collection, confirming that the megaplasmid is indeed a plasmid encoding non-obligatory functional traits. The divergent GC content and codon usage of the megaplasmid suggest a non-Vibrio origin. The genetic diversity found in the six investigated megaplasmid sequences indicates adaptation within the different Vibrio hosts. Although many of the megaplasmid genes could not be categorised through Cluster of Orthologous Genes (COG) classification, genes coding for partitioning systems, type IV secretion systems, defence systems, and toxin-antitoxin modules were identified. These contribute to a high plasmid stability, as we demonstrated by the curing experiments performed with our strains. Consequently, the megaplasmid described here represents a highly stable but adaptive genetic element that is characterised by as yet unexplored genetic traits.

副溶血性弧菌是一种与海洋有关的细菌，以前曾与食用海产品引起的食源性疾病有关。各种含有抗菌素耐药性和毒力基因的质粒已被描述为副溶血性弧菌。通过全基因组测序，我们发现两个副溶血性弧菌菌株含有一个大的额外的圆形基因组元件，为0.882 Mbp。NCBI数据库搜索显示，该元素代表了一种罕见但全球分布的巨质粒，在另外四种弧菌菌株中检测到，跨越不同的物种（副溶血性弧菌、霍乱弧菌和创伤弧菌）、地理来源和宿主。除了从我们的研究中发现的两个含有副溶血性v的巨型质粒外，我们还在菌株收集中发现了两个无巨型质粒的等基因菌株，证实了巨型质粒确实是一个编码非强制性功能性状的质粒。巨质粒的GC含量和密码子使用的差异表明其非弧菌起源。在六个研究的巨质粒序列中发现的遗传多样性表明在不同弧菌宿主内的适应性。尽管许多巨质粒基因无法通过同源基因簇（COG）分类进行分类，但已鉴定出编码分配系统、IV型分泌系统、防御系统和毒素-抗毒素模块的基因。这些有助于高质粒的稳定性，正如我们用我们的菌株进行的固化实验所证明的那样。因此，这里描述的巨型质粒代表了一种高度稳定但适应性强的遗传元素，其特征是尚未探索的遗传特征。

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引用次数: 0

A Tribute to Manolo Espinosa 致敬马诺洛·埃斯皮诺萨

IF 2.2 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-09-01 DOI: 10.1016/j.plasmid.2025.102758

Gloria del Solar , Christopher M. Thomas , Elisabeth Grohmann

引用次数: 0

Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids 基于组装的婴儿肠道微生物组分析揭示了新的普遍存在的质粒。

IF 2.2 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-09-01 DOI: 10.1016/j.plasmid.2025.102761

Hanna Theodora Noordzij , Meike T. Wortel , Anna Heintz-Buschart , Patricija Petrikonyte , Eric J. de Muinck , Pål Trosvik

Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.

人们对诸如婴儿肠道微生物群等自然生态系统中可移动遗传元素的作用知之甚少。在这里，我们通过分析12名婴儿从出生到一岁的每月粪便样本，对婴儿质粒进行了迄今为止最全面的纵向研究。我们采用基于组装的生物信息学管道来重建和鉴定全长质粒，包括一种新的方法来分配假定的质粒宿主。然后我们研究了婴儿肠道微生物组的质粒含量和动态。经过组装和鉴定，我们在婴儿队列中鉴定出620个独特的环状质粒，包括一些新的序列。在几个样本和婴儿中独立组装相同的质粒有助于证实质粒的真实性。在观察到的质粒中，有最近发现的普遍存在且丰富的拟杆菌质粒pBI143。总体而言，拟杆菌属的质粒携带量最高，而梭状芽孢杆菌属的质粒多样性最高，包括5种以前未知的广泛分布的质粒。最后，我们利用数据集的纵向性质来研究质粒丰度和物种动态的时间变化之间的同期相关性。这使我们能够在每个婴儿中连接共同居住的质粒和紧密连接的质粒分类单元对。这些对质粒生态学的见解有助于我们理解在复杂微生物群落中驱动质粒分布的决定因素。

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引用次数: 0

Expression, purification, and refolding of an optimized SARS-CoV-2 receptor binding domain in E. coli 优化的SARS-CoV-2受体结合域在大肠杆菌中的表达、纯化和重折叠

IF 2.2 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-09-01 DOI: 10.1016/j.plasmid.2025.102760

Anamika Biswas, Arighna Sarkar, Sreejith Raran-Kurussi, Kalyaneswar Mandal

The outbreak of Coronavirus Disease 2019 (COVID-19) has posed a significant risk to global health, warranting the formulation of efficient preventive and therapeutic measures to tackle its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of coronaviruses plays a pivotal role in viral attachment and entry into host cells. The receptor-binding domain (RBD) of the SARS-CoV-2 S protein has demonstrated a robust binding affinity to ACE2 receptors in humans. Consequently, it has become a prime target for therapeutic interventions using antibodies, vaccines, or other designed inhibitors. We engineered an RBD sequence with refined ORF boundaries guided by structural insights, which enabled efficient in vitro refolding. This highlights the critical role of precise expression cassette design in a plasmid, extending beyond conventional parameters such as promoter or fusion tag selection. Using customized refolding procedures, we obtained 10–12 mg of active protein from a one-liter LB culture. The biological activity of the refolded RBD was confirmed by monitoring its interaction with the designed LCB1 miniprotein ligand by surface plasmon resonance, wherein they exhibited significant affinity levels as reflected by their dissociation constants (K_D values <10 nM). The resulting RBD could be an ideal target for designing potent COVID-19 antivirals.

2019冠状病毒病（COVID-19）的爆发对全球健康构成重大风险，有必要制定有效的预防和治疗措施，以应对其病原体严重急性呼吸系统综合征冠状病毒2 （SARS-CoV-2）。冠状病毒的刺突(S)蛋白在病毒附着和进入宿主细胞中起着关键作用。sars - cov - 2s蛋白的受体结合结构域（RBD）在人体内显示出与ACE2受体的强大结合亲和力。因此，它已成为使用抗体、疫苗或其他设计抑制剂进行治疗干预的主要目标。我们设计了一个RBD序列，在结构见解的指导下，具有精确的ORF边界，从而实现了有效的体外重折叠。这突出了质粒中精确表达盒设计的关键作用，超出了启动子或融合标签选择等传统参数。使用定制的折叠程序，我们从一升LB培养物中获得10-12毫克活性蛋白。通过表面等离子体共振监测其与设计的LCB1微小蛋白配体的相互作用，证实了重组RBD的生物活性，其中它们的解离常数（KD值<；10 nM）反映了它们具有显著的亲和力水平。由此产生的RBD可能是设计有效的COVID-19抗病毒药物的理想靶标。

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引用次数: 0

Single-strain mobilome sequencing quantifies bacterial genetic response to stress, including activity of IS elements, prophages, RNAs, and REPINs. 单菌株移动组测序量化细菌对应激的遗传反应，包括IS元件、前噬菌体、rna和REPINs的活性。

IF 2.2 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-09-01 DOI: 10.1016/j.plasmid.2025.102759

Tue Kjærgaard Nielsen, Lars Hestbjerg Hansen

Microbial genomes are continuously being rearranged by mobile genetic elements (MGEs), leading to configurations that may confer novel phenotypic traits such as antibiotic resistance, degradation of compounds, or metabolic features. Standard genomic sequencing provides a snapshot of a genome in one configuration, but this static image does not give insight into the dynamics of genomic evolution and whether MGEs are actively changing a genome. We applied single-strain mobilome sequencing to Escherichia coli K-12 MG1655 under various stress conditions: UV, SDS, nalidixic acid, tetracycline, cetrimide, and copper. Under these conditions, we quantified the activity of a range of genetic elements, including extrachromosomal circular DNA (eccDNA) from IS elements, RNA genes, the UV-inducible e14 prophage, and intergenic repetitive sites (REP). Of the stressors, copper and SDS are among the largest inducers of eccDNA formation from some IS elements, while elevated levels of hypothetical RNA/DNA heteroduplexes of ribosomal and transfer RNAs, and Rhs-nuclease proteins are induced under various stressors, especially copper and SDS. This approach holds promise for quantifying the genetic response to environmental stress and implications for genome plasticity. The mobilization of IS elements upon copper and other stressors helps to explain co-selection of heavy metals with antibiotic resistance genes and MGEs.

微生物基因组不断被移动遗传元件（MGEs）重新排列，导致可能赋予新的表型特征的结构，如抗生素耐药性、化合物降解或代谢特征。标准的基因组测序提供了基因组在一种结构中的快照，但这种静态图像并不能深入了解基因组进化的动态以及MGEs是否正在积极地改变基因组。我们对大肠杆菌K-12 MG1655在不同的胁迫条件下进行了单株移动组测序：紫外、SDS、萘啶酸、四环素、氰胺和铜。在这些条件下，我们量化了一系列遗传元件的活性，包括来自IS元件的染色体外环状DNA （eccDNA）、RNA基因、uv诱导的e14噬菌体和基因间重复位点（REP）。在应激源中，铜和SDS是一些IS元件形成eccDNA的最大诱导剂，而在各种应激源下，尤其是铜和SDS，可诱导核糖体和转移RNA的假想RNA/DNA异双链和rhs -核酸酶蛋白水平升高。这种方法有望量化遗传对环境压力的反应和对基因组可塑性的影响。IS元素在铜和其他应激源上的动员有助于解释重金属与抗生素抗性基因和MGEs的共选择。

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引用次数: 0

Insights from public database sequences related to the replication initiation protein TrfA of the IncP-1 plasmid RK2 来自IncP-1质粒RK2复制起始蛋白TrfA的公共数据库序列的见解。

IF 2.2 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-08-16 DOI: 10.1016/j.plasmid.2025.102756

Haruo Suzuki , Kazuki Moriguchi , Masaki Shintani , Masato Suzuki , Hideaki Nojiri

Replicon typing identifies sequences similar to known DNA replication initiators and is widely used to detect specific plasmid groups (e.g., IncP-1) in genome and metagenome sequencing data. However, the characteristics of these homologous sequences in public databases have not been systematically assessed, making it difficult to determine whether detecting a specific replicon type reliably indicates the presence of a particular plasmid group. Here, we conducted amino acid sequence alignments to identify sequences similar to the replication initiation protein TrfA of the IncP-1 plasmid RK2 in the NCBI non-redundant (nr) database. In the nr nucleotide database, TrfA-matched nucleotide sequences were found across diverse taxonomic groups and replicons, including complete and partial plasmids and chromosomes. In total, 76 protein sequences from the reference plasmid RK2 were screened against the nucleotide sequences of the trfA-harboring plasmids to identify candidate IncP-1 plasmids. TrfA-related proteins, originating from bacterial chromosomes, plasmids, and phages, were selected from the nr amino acid database and used to infer phylogenetic trees. Our phylogenetic analyses reveal that TrfA homologs have diverged through vertical inheritance within IncP-1 and horizontal gene transfer across replicons and taxa. These findings caution against overreliance on single-gene replicon typing to infer plasmid group identity from sequence data.

复制子分型识别与已知DNA复制启动子相似的序列，并广泛用于检测基因组和宏基因组测序数据中的特定质粒群（例如IncP-1）。然而，公共数据库中这些同源序列的特征尚未得到系统评估，因此很难确定检测到特定复制子类型是否可靠地表明存在特定的质粒群。在这里，我们进行了氨基酸序列比对，以确定与NCBI非冗余（nr）数据库中IncP-1质粒RK2的复制起始蛋白TrfA相似的序列。在nr核苷酸数据库中，在不同的分类群和复制子中发现了trfa匹配的核苷酸序列，包括完整的和部分的质粒和染色体。从参比质粒RK2中提取76个蛋白序列，与携带trfa的质粒核苷酸序列进行比对，鉴定候选IncP-1质粒。trfa相关蛋白来自细菌染色体、质粒和噬菌体，从nr氨基酸数据库中选择，用于推断系统发育树。我们的系统发育分析表明，TrfA同源物通过IncP-1内部的垂直遗传和复制子和分类群之间的水平基因转移而分化。这些发现提醒人们不要过度依赖单基因复制子分型来从序列数据推断质粒群的身份。

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引用次数: 0

Prevention of RK2 plasmid replication initiation in starved Escherichia coli cells 饥饿大肠杆菌细胞中RK2质粒复制起始的预防

IF 1.8 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-07-20 DOI: 10.1016/j.plasmid.2025.102755

Ewelina Boguszewska , Igor Konieczny

Bacterial adaptation to environmental stress involves stringent regulation of DNA replication. While the mechanisms controlling chromosomal replication under adverse conditions, such as amino acid starvation, are relatively well characterized, the molecular basis for stress-induced inhibition of plasmid replication remains largely unknown. In this study, we investigated how amino acid starvation affects the replication of the broad-host-range RK2 plasmid in Escherichia coli, focusing on the plasmid-encoded replication initiator TrfA and host-encoded initiator DnaA. We found that the RK2 plasmid origin of replication (oriV) occupation by TrfA and DnaA is prevented in stress conditions. We also did not detect increase of plasmid DNA level showing that new rounds of RK2 replication are not initiated. The replication-inactive state persisted even in cells expressing a hyperactive monomeric TrfA variant that is incapable of handcuffing, indicating that other regulatory mechanisms, beyond handcuffing, contribute to the prevention of the plasmid replication. The reduction of initiators binding to the plasmid origin during stress coincided with a substantial decrease in the intracellular levels of TrfA, as shown in this study, and of DnaA, as reported previously. Given that cell division is arrested during stress, the only explanation for the observed gradual decrease of TrfA levels is proteolysis. Our findings demonstrate that during amino acids starvation, RK2 plasmid replication in E. coli is likely prevented by a significant drop in initiator proteins concentrations. This uncovers a previously underappreciated layer of plasmid replication control under stress conditions.

细菌对环境压力的适应涉及严格的DNA复制调节。虽然在不利条件下控制染色体复制的机制，如氨基酸饥饿，已经得到了很好的表征，但应激诱导的质粒复制抑制的分子基础仍然很大程度上未知。在这项研究中，我们研究了氨基酸饥饿如何影响大肠杆菌中宽宿主范围RK2质粒的复制，重点研究了质粒编码的复制启动子TrfA和宿主编码的启动子dna。我们发现RK2质粒起源的复制（oriV）被TrfA和dna占领在胁迫条件下被阻止。我们也没有检测到质粒DNA水平的增加，这表明新一轮的RK2复制没有开始。这种复制不活跃状态甚至在表达一种无法被铐住的高活性单体TrfA变体的细胞中也持续存在，这表明除了铐住外，还有其他调节机制有助于阻止质粒复制。在胁迫期间，与质粒起源结合的启动子减少，与细胞内TrfA水平的大幅下降（如本研究所示）和dna水平的大幅下降（如先前报道）相一致。考虑到细胞分裂在压力下被阻止，TrfA水平逐渐下降的唯一解释是蛋白质水解。我们的研究结果表明，在氨基酸缺乏的情况下，RK2质粒在大肠杆菌中的复制可能会被引发蛋白浓度的显著下降所阻止。这揭示了在胁迫条件下质粒复制控制的一个先前未被重视的层面。

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引用次数: 0

Strategies for zygotic gene expression during plasmid establishment 质粒建立过程中合子基因表达策略。

IF 1.8 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-06-26 DOI: 10.1016/j.plasmid.2025.102754

Nathan Fraikin , Bruria Samuel , David Burstein , Christian Lesterlin

Conjugative plasmids are key drivers of horizontal gene transfer and the spread of antimicrobial resistance. Their successful establishment in new hosts requires overcoming diverse bacterial defence mechanisms, such as restriction-modification systems, CRISPR-Cas systems, and the SOS response. Plasmids achieve this through a leading region-encoded zygotic program of anti-defence genes expressed early in conjugation. This program employs diverse strategies, including single-stranded promoters, repressed double-stranded promoters, and protein translocation. This review explores the diversity of these zygotic programs, the mechanisms underlying their timely regulation, and the array of anti-defence functions they encode. Further investigation of leading region genes is crucial for discovering novel counter-defence strategies and understanding their tailored regulation across diverse plasmid and bacterial species, ultimately enabling us to better understand and potentially manipulate plasmid transfer.

共轭质粒是水平基因转移和抗菌素耐药性传播的关键驱动因素。它们在新宿主体内的成功建立需要克服多种细菌防御机制，如限制性修饰系统、CRISPR-Cas系统和SOS反应。质粒通过在接合早期表达的抗防御基因的一个领先的区域编码合子程序来实现这一点。该程序采用多种策略，包括单链启动子、抑制双链启动子和蛋白质易位。这篇综述探讨了这些合子程序的多样性，其及时调节的机制，以及它们编码的一系列抗防御功能。对前导区基因的进一步研究对于发现新的反防御策略和理解它们在不同质粒和细菌物种中的定制调节至关重要，最终使我们能够更好地理解和潜在地操纵质粒转移。

引用次数: 0

Discovery and assembly of plasmids in the fish pathogen Tenacibaculum 鱼病原体腱藻质粒的发现与组装。

IF 1.8 4区生物学 Q3 GENETICS & HEREDITY

Plasmid

Pub Date : 2025-06-18 DOI: 10.1016/j.plasmid.2025.102753

Ashton N. Sies , Joseph P. Nowlan , Laura J. Schnell , John S. Lumsden , Spencer Russell , Andrew D.S. Cameron

Members of the marine bacterial genus Tenacibaculum cause disease in finfish and outbreaks result in significant animal harm and losses in aquaculture around the globe. Plasmids have not been previously identified in Tenacibaculum, but long-read DNA sequencing of genomes from disease-associated Tenacibaculum isolates collected between 2017 and 2020 in British Columbia, Canada, revealed circular putative plasmids in three Tenacibaculum species. In addition to high-quality circular assembly, the putative plasmids contained genes encoding plasmid replication, mobility, and partitioning proteins. Genes for type B conjugation machinery and type 6_iii secretion system components were also identified on each of the two largest plasmid sequences. Several protocols were tested to visualize and enrich Tenacibaculum plasmid DNA. Rolling-circle replication with Phi29 DNA polymerase amplified putative plasmids smaller than 100 kb. Alkaline lysis extraction provided weak enrichment of putative plasmid DNA, but plasmids could not be confidently resolved by Eckhardt extraction and electrophoresis in agarose gels. The newly assembled plasmids matched previously sequenced Tenacibaculum contigs, suggesting that publicly available Tenacibaculum genomes contain unrecognized plasmids. The discovery of putative plasmids in Tenacibaculum is significant because plasmids often confer important functions to host cells and serve as vehicles for horizontal gene transfer within and beyond the host bacterial species.

海洋细菌tenacacbaculum属的成员可引起鱼类疾病，其爆发对全球水产养殖造成重大动物伤害和损失。此前在Tenacibaculum中未发现质粒，但对2017年至2020年在加拿大不列颠哥伦比亚省收集的与疾病相关的Tenacibaculum分离株基因组的长读DNA测序显示，在三种Tenacibaculum物种中发现了环状质粒。除了高质量的环状组装外，假定的质粒还含有编码质粒复制、迁移和分配蛋白质的基因。在两个最大的质粒序列上也分别鉴定了B型偶联机制和6iii型分泌系统成分的基因。几种方案进行了测试，以可视化和丰富tenacacibaculum质粒DNA。用Phi29 DNA聚合酶进行滚圈复制，扩增出小于100 kb的推定质粒。碱性裂解提取提供了假定质粒DNA的弱富集，质粒不能通过Eckhardt提取和琼脂糖凝胶电泳可靠地分离。新组装的质粒与先前测序的Tenacibaculum contigs匹配，突出表明公开可用的Tenacibaculum基因组含有未被识别的质粒。质粒的发现具有重要意义，因为质粒通常赋予宿主细胞重要的功能，并作为宿主物种内外水平基因转移的载体。

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引用次数: 0