Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements

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Toxins-antitoxins: diversity,evolution and function

Genes for toxin-antitoxin (TA) complexes are widespread in prokaryote genomes, and species frequently possess tens of plasmid and chromosomal TA loci. The complexes are categorized into three types based on genetic organization and mode of action. The toxins universally are proteins directed against specific intracellular targets, whereas the antitoxins are either proteins or small RNAs that neutralize the toxin or inhibit toxin synthesis. Within the three types of complex, there has been extensive evolutionary shuffling of toxin and antitoxin genes leading to considerable diversity in TA combinations. The intracellular targets of the protein toxins similarly are varied. Numerous toxins, many of which are sequence-specific endoribonucleases, dampen protein synthesis levels in response to a range of stress and nutritional stimuli. Key resources are conserved as a result ensuring the survival of individual cells and therefore the bacterial population. The toxin effects generally are transient and reversible permitting a set of dynamic, tunable responses that reflect environmental conditions. Moreover, by harboring multiple toxins that intercede in protein synthesis in response to different physiological cues, bacteria potentially sense an assortment of metabolic perturbations that are channeled through different TA complexes. Other toxins interfere with the action of topoisomersases, cell wall assembly, or cytoskeletal structures. TAs also play important roles in bacterial persistence, biofilm formation and multidrug tolerance, and have considerable potential both as new components of the genetic toolbox and as targets for novel antibacterial drugs.     

携带污染物降解基因的可移动基因元件及其介导的生物修复

可移动基因元件(mobile genetic elements,MGEs)在环境微生物群落中的水平转移是细菌基因组进化和适应特定环境压力的重要机制.在污染土壤和水体中接种携带具有降解基因MGEs的菌株后,随着MGEs的水平基因转移,可使降解基因转移至具有竞争性的土著微生物中并在其中表达,从而不必考虑供体菌在环境中是否能够长期存活.这种由可移动降解基因元件水平转移介导的生物修复为探索新的生物修复途径提供了可行性.本文重点综述了环境样品中携带降解基因MGEs的多样性及其在促进污染物降解过程中的重要作用,介绍了从环境样品中分离代谢MGEs的方法,并列举了在污染土壤、活性污泥、其他生物反应器等生态系统中MGEs水平转移的几个实例.     

昆虫水平基因转移及其研究进展

水平基因转移(horizontal gene transfer, HGT)是生物体获得遗传信息的方式之一,对生物体进化起重要作用。近年来,越来越多昆虫中的水平基因转移现象被报道,如在鳞翅目(如家蚕、甜菜夜蛾、小菜蛾、斜纹夜蛾)、半翅目(如柑橘粉蚧、烟粉虱)、鞘翅目(如咖啡果小蠹、米象、光肩星天牛)、膜翅目(如金小蜂)、双翅目(如果蝇、白纹伊蚊)等昆虫中广泛存在水平转移基因,且不同的水平转移基因对昆虫的营养合成与共生、吸收与消化、毒素产生与解毒、生长和发育、体色改变等方面有着重要作用。本文结合国内外专家学者的相关报道,就HGT的研究步骤与技术方法、评判HGT发生的方法、昆虫HGT的供体与功能几个方面进行了总结和讨论,以期更加深入地了解水平基因转移现象,为探究水平基因转移的作用机制、理解昆虫的进化、遗传和行为、并将水平基因转移应用到农业生产中为农业害虫的绿色防治提供更多思路。     

环境中抗生素抗性基因的水平传播扩散

抗生素抗性基因作为一类新型环境污染物,其在不同环境介质中的传播扩散可能比抗生素本身的环境危害更大,其中,水平基因转移是抗生素抗性基因传播的重要方式,是造成抗性基因环境污染日益严重的原因之一.本文系统阐述了抗生素抗性基因在环境中发生水平转移的主要分子传播元件及其影响因素,这对于正确揭示抗性基因的分子传播机制具有重要意义.结合多重抗药性的传播扩散机制,探讨了行之有效的遏制抗生素抗性基因传播扩散的方法和途径,并针对目前的污染现状,对今后有关抗生素抗性基因水平转移的研究重点进行了展望.     

综述与专论：微生物消毒剂抗性机理

在物体表面和传播介质中,消毒剂能有效抑制或杀死微生物,广泛用于食品、卫生、健康、防疫等领域。在新型冠状病毒肺炎(COVID-19)疫情期间,全球消毒剂的使用量激增,对有效防控病毒传播和防止疫情扩散起到重要作用。但消毒剂的不正确使用会降低其有效性,甚至会诱导微生物产生抗性,从而增加传染性疾病的传播风险。微生物的消毒剂抗性基因还会通过繁殖传代增殖或在不同种属间水平转移而加剧其污染和传播风险,严重威胁到公共卫生安全。目前,抗生素抗性基因(ARG)的广泛出现引起了全球对公共卫生的关注,但对消毒剂的抗性认识非常有限。本文综述了近年来微生物对消毒剂抗性的研究,着重就微生物通过形成生物膜、降低细胞膜通透性、过量表达外排泵、产生消除或减弱消毒剂的特异性酶、改变作用靶点等方式产生抗性的机理进行综述。另外针对微生物消毒剂抗性的获得和传播,对染色体和质粒介导的抗性基因、环境中微生物消毒剂抗性与抗生素抗性的关联进行了论述。消毒剂抗性基因能通过质粒、噬菌体等可移动遗传元件,以转化、转导或接合的方式转移传播,对科学消毒提出新要求。     

微生物消毒剂抗性机理

在物体表面和传播介质中,消毒剂能有效抑制或杀死微生物,广泛用于食品、卫生、健康、防疫等领域.在新型冠状病毒肺炎(COVID-19)疫情期间,全球消毒剂的使用量激增,对有效防控病毒传播和防止疫情扩散起到重要作用.但消毒剂的不正确使用会降低其有效性,甚至会诱导微生物产生抗性,从而增加传染性疾病的传播风险.微生物的消毒剂抗性...     

Enterococcal biofilm—A nidus for antibiotic resistance transfer?

Enterococci, which are on the WHO list of priority pathogens, are commonly encountered in hospital acquired infection and are becoming increasing significant due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment, and their presence is frequently used as an indicator of faecal pollution. Their success is related to their ability to survive within a broad range of habitats and the ease by which they acquire mobile genetic elements, including plasmids, from other bacteria. The enterococci are frequently present within a bacterial biofilm, which provides stability and protection to the bacterial population along with an opportunity for a variety of bacterial interactions. Enterococci can accept extrachromosomal DNA both from within its own species and from other bacterial species, and this is enhanced by the proximity of the donor and recipient strains. It is this exchange of genetic material that makes the role of biofilms such an important aspect of the success of enterococci. There remain many questions regarding the most suitable model systems to study enterococci in biofilms and regarding the transfer of genetic material including antibiotic resistance in these biofilms. This review focuses on some important aspects of biofilm in the context of horizontal gene transfer (HGT) in enterococci.     

The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes

We have found direct DNA repeats 21–47 bp in length interspersed with nonrepetitive sequences of similar length, or clustered regularly interspaced short palindromic repeats (CRISPRs) in a wide range of diverse prokaryotes, including many Archaeal and Eubacterial species. A number of cas, CRISPR-associated genes have also been characterized in many of the same organisms. Phylogenetic analysis of these cas genes suggests that the CRISPR loci have been propagated via HGT, horizontal gene transfer. We suggest a mechanism by which this HGT has occurred, namely, that the CRISPR loci can be carried between cells on megaplasmids ≥40 kb in length. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Stuart Newfeld]     

利用CRISPR-Cas系统防控细菌耐药性的研究进展

细菌多重耐药是医药健康、农林牧渔、生态环境等多领域共同面临的全球性挑战.抗生素耐药基因跨物种跨区域传播是导致细菌多重耐药形成的重要原因.然而,目前尚无有效方案解决日益严峻的细菌多重耐药问题.由规律成簇间隔短回文重复序列和与之相关的蛋白组成的CRISPR-Cas系统,可靶向切割进入细菌的外源核酸,具有防控耐药基因转移导致...     

Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli–Shigella genetic exchange communities

Genetic material can be transmitted not only vertically from parent to offspring, but also laterally (horizontally) from one bacterial lineage to another. Lateral genetic transfer is non-uniform; biases in its nature or frequency construct communities of genetic exchange. These biases have been proposed to arise from phylogenetic relatedness, shared ecology and/or common lifestyle. Here, we test these hypotheses using a graph-based abstraction of inferred genetic-exchange relationships among 27 Escherichia coli and Shigella genomes. We show that although barriers to inter-phylogenetic group lateral transfer are low, E. coli and Shigella are more likely to have exchanged genetic material with close relatives. We find little evidence of bias arising from shared environment or lifestyle. More than one-third of donor–recipient pairs in our analysis show some level of fragmentary gene transfer. Thus, within the E. coli–Shigella clade, intact genes and gene fragments have been disseminated non-uniformly and at appreciable frequency, constructing communities that transgress environmental and lifestyle boundaries.     

Diverse symbiovars nodulating cowpea (Vigna unguiculata L. Walp.) in highly adaptable agro-ecological zones in Mozambique

The presence of effective microsymbionts in the soil and their compatibility with the host plant are the key determinants to the N₂ fixation process. In Sub-Saharan Africa, nitrogen fixation in locally adapted cowpea and the distribution of their symbiovars are not well understood. The Aim of the study was to assess the distribution and symbiotic phylogenetic position of cowpea microsymbionts. Root nodules were sampled from various cowpea genotypes planted in Agro-Ecological Zone 7 and 8 (AEZ 7 and AEZ 8). Root-nodule bacteria were isolated and their molecular characterization was conducted. Physicochemical properties of soil were recorded. Enterobacterial Repetitive Intergenic Consensus (ERIC) distribution patterns in rhizobial genomes resulted in genetically diverse rhizobial population in Northern Mozambique. Principal component analysis showed that location-specific soil environment determined the presence of particular microsymbionts. Based on 16S rRNA and symbiotic gene analysis many diverse symbiovars were found in Mozambican soils. With few discrepancies, the results further confirmed the coevolution of the nifH, nodD, nodC and nodY/K genes, which was indicative of natural events such as vertical/horizontal gene transfer. The results suggested that ecological and phylogenetic studies of the microsymbionts are necessary to better reflect symbiovar identification and the ecological adaptation of the cowpea-nodulating rhizobial community.     

Novel integrative elements and genomic plasticity in ocean ecosystems

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