基因强化在难降解污染物生物处理和修复中的应用

基因强化通过强化降解基因在土著菌群中的水平迁移和传播, 促进土著降解菌群的进化, 改善基因工程菌生物强化作用的稳定性, 提高难降解污染物的生物去除效果。介绍了基因强化的原理-微生物群落内水平基因迁移, 讨论了基因载体、细胞接触条件和环境条件等影响基因强化的因素, 综述了目前基因强化在土壤生物修复和废水生物处理中的应用现状, 并提出了基因强化中存在的问题。     

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.     

基因强化在难降解污染物生物处理和修复中的应用

基因强化通过强化降解基因在土著菌群中的水平迁移和传播,促进土著降解菌群的进化,改善基因工程菌生物强化作用的稳定性,提高难降解污染物的生物去除效果.介绍了基因强化的原理-微生物群落内水平基因迁移,讨论了基因载体、细胞接触条件和环境条件等影响基因强化的因素,综述了目前基因强化在土壤生物修复和废水生物处理中的应用现状,并提出了基因强化中存在的问题.     

降解强致癌性有机污染物的微生物

多氯联苯(PCB)是强致癌有机污染物之一,是潜在的致癌因子,这类化合物有209种之多,其中某些化合物具有类似二噁英(dioxin)的毒性如六氯联苯等。有些微生物对PCB有降解作用,如G^ 细菌(指革氏阳性菌)中有园红球菌(Rhodococcus globerulus)也称球状红球菌,还有红串红球菌(Rh．erythropolis)、芽孢杆菌(Bacillus sp．)野生株以及该两属其他未定名菌株均表现对PCB等的降解活力,     

细菌对环境污染物的趋化性及其在生物修复中的作用

细菌对有机化合物的降解能力是一种利用碳源和能源的优势,这种能力可以用来设计安全、有效和无二次污染的污染物的生物修复系统。趋化性是细菌适应外界化学环境变化而作出的行为反应,是一种寻找碳源和能源的优势。细菌的趋化性能够增强细菌在自然环境中的降解污染物的效果,细菌的趋化性与降解性之间的关系研究已经成为热点。介绍了细菌的趋化性的基本概念和趋化信号转导的机制,重点讨论了细菌对环境污染化合物的趋化性,从基因水平揭示了趋化性与降解性之间的紧密联系,认为趋化性可以有效地促进降解性细菌对污染物的生物修复作用。     

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。     

环境中生物膜的菌群结构与污染物降解特性

生物膜是细菌最常见的生长方式。结构有序、功能分化的生物膜群落为内部细菌提供在不利环境中生存的庇护,其环境功效也日益受到关注。本文综述了多种环境中微生物与不同材料表面相互作用、进而发展为生物膜的机制;介绍了环境工程领域中生物膜的先锋菌种和菌群结构动态变化;介绍了生物膜在污染环境中的抗逆与降解特性。     

微生物燃料电池对污染物的强化降解及其机理综述

产电和污染物降解是微生物燃料电池(Microbial Fuel Cells,MFCs)的两个基本功能,也是MFCs作为一种新型的环境治理和能源技术最具吸引力的优势。大量的研究已表明:相对于一般厌氧生物降解技术,MFCs具有更高效的废弃物、废水或污染物降解的能力。解析MFCs强化污染物降解的机理对于进一步优化MFCs的性能具有重要的指导意义,也可以为MFCs在实际环境中的原位应用提供理论支持。本文在综述MFCs强化污染物降解研究报道的基础上,从MFCs中微生物群落的代谢模式、生物膜的活性以及MFCs对局部氧化还原环境的影响等方面为MFCs强化污染物降解的功能提供可能的理论依据,并对MFCs在污染物降解方面的几个可能的发展方向进行展望,为不同学科背景的相关研究者提供参考。     

昆虫的水平基因转移研究

水平基因转移是一种能够在物种间进行基因交流的现象,是生物迅速适应环境的主要驱动力之一.近年来,随着测序技术的进步,昆虫中的水平基因转移现象被大量报道,成为昆虫研究的热点之一.本文总结了水平基因转移研究的常用流程和手段,以及昆虫水平转移基因的供体、受体和功能,讨论水平基因转移与昆虫食性的联系以及研究方法的局限,并展望昆虫水平基因转移研究领域未来的方向.     

柴油降解细菌的分离及其降解能力初探

从含油土壤中,筛选出能以0#柴油为惟一碳源的2株柴油降解菌,经鉴定分别为假单胞菌(Pseudomonoussp.)和芽孢杆菌(Bacillussp.)。通过其降解能力的测试,假单胞杆菌属细菌A8的降解能力较强;在含油浓度ρ=10g/L的摇瓶试验中,培养7d后其除油率分别为18%和31%。在含油浓度1%的土壤中,2株菌均能正常生长和繁殖,接种30d除油率分别为35%和48.3%。     

水平基因转移

简要介绍了水平基因转移（horizontal gene transfer,HGT）的基本概念以及进行转移的主要方式：由质粒或病毒等介导的水平基因转移和基因的“直接”水平转移。并结合基因组序列分析,重点阐述远缘生物之间发生的广泛的基因交流,以及其与进化、系统发育和基因工程生物安全性问题的探讨。 Abstract:In this paper the conception of horizontal gene transfer (HGT) was introduced,and main mode of HGT was also enumerated as follows:HGT by medium such as plasmid and virus etc.and the HGT without any medium.The transfer of genes from one species to another especially between remote species was emphasized by the information from genome sequencing.The problems about evolution phylogenies and safety of GEMs (gene engineered microorganisms) for HGT were discussed.     

Horizontal Gene Transfer: A Universal Phenomenon

According to the scientific literature, it is reasonable to consider that lateral transfer of genes is an usual mechanism of adaptation of the biological organisms to environmental stresses. Furthermore, from bacteria to cultured human cells, including fungi and plants, a large diversity of horizontal gene transfers—natural or artificial, experimental or deduced from sequence analysis—have been described. Therefore, the uncharacterized biodiversity—particularly in microbiology—associated with the universality of the horizontal gene transfer phenomenon leads to the consideration that dissemination of DNA from Genetically Modified Organisms (GMO) in biological environments, including food and soil, is uncontrolled and predictable.     

Molecular Variation and Horizontal Gene Transfer of the Homocysteine Methyltransferase Gene mmuM and its Distribution in Clinical Pathogens

The homocysteine methyltransferase encoded by mmuM is widely distributed among microbial organisms. It is the key enzyme that catalyzes the last step in methionine biosynthesis and plays an important role in the metabolism process. It also enables the microbial organisms to tolerate high concentrations of selenium in the environment. In this research, 533 mmuM gene sequences covering 70 genera of the bacteria were selected from GenBank database. The distribution frequency of mmuM is different in the investigated genera of bacteria. The mapping results of 160 mmuM reference sequences showed that the mmuM genes were found in 7 species of pathogen genomes sequenced in this work. The polymerase chain reaction products of one mmuM genotype ({"type":"entrez-nucleotide","attrs":{"text":"NC_013951","term_id":"291289198","term_text":"NC_013951"}}NC_013951 as the reference) were sequenced and the sequencing results confirmed the mapping results. Furthermore, 144 representative sequences were chosen for phylogenetic analysis and some mmuM genes from totally different genera (such as the genes between Escherichia and Klebsiella and between Enterobacter and Kosakonia) shared closer phylogenetic relationship than those from the same genus. Comparative genomic analysis of the mmuM encoding regions on plasmids and bacterial chromosomes showed that pKF3-140 and pIP1206 plasmids shared a 21 kb homology region and a 4.9 kb fragment in this region was in fact originated from the Escherichia coli chromosome. These results further suggested that mmuM gene did go through the gene horizontal transfer among different species or genera of bacteria. High-throughput sequencing combined with comparative genomics analysis would explore distribution and dissemination of the mmuM gene among bacteria and its evolution at a molecular level.     

水平基因转移介导抗菌素耐药性传播机制的研究进展

近几十年来,病原菌耐药性的出现和蔓延已上升为严峻的公共卫生问题。越来越多研究表明,抗菌素抗性基因(antibiotic resistance genes,ARGs)不仅仅见于临床所分离的病原体,而是包括所有的致病菌、共生菌以及环境中的细菌,它们都能在可移动遗传元件和噬菌体的作用下,通过水平基因转移(horizontal gene transfer,HGT)途径获得耐药性,进而形成抗菌素耐药基因簇(耐药基因组)。HGT可导致抗菌素的耐药性在环境共生菌和病原菌之间传播扩散,这可通过临床上一些重要的抗菌素耐药基因的传播证实。传统观念认为HGT的三种机制中,接合对ARGs的传播影响最大,最近研究表明转化和转导对ARGs播散起到不可忽视的作用。通过深入了解耐药基因组的传播及其在动员病原菌耐药中发挥的作用,对于控制这些基因的播散是至关重要的。将讨论耐药基因组的概念,提供临床相关的抗菌素抗性基因水平基因转移的例子,对当前已研究的促使抗菌素耐药性传播的各种HGT机制进行回顾。     

Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria

Protein posttranslational modifications add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms, and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologs. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than 1 billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared with products of likely endosymbiont gene transfer, mitochondrial proteins, and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.     

Horizontal Transfer of Mercury Resistance Genes in Environmental Bacterial Populations

The results of studying the horizontal transfer of mercury resistance determinants in environmental bacterial populations are reviewed. Identical or highly homologous mercury resistance (mer) operons and transposons were found in bacteria of different taxonomic groups from geographically distant regions. Recombinant mer operons and transposons were revealed. The data suggest high frequencies of horizontal transfer and of recombination for mercury resistance determinants. The mechanisms of horizontal gene transfer were elucidated in Gram-negative and Gram-positive bacteria. New transposons were found and analyzed.     

Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer

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Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees

We suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. The search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. Numeric values are introduced to measure the discrepancy between the trees. This approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. This resulted in a list of the candidate genes for which the hypothesis of horizontal transfer in evolution looks true.     

Horizontal Gene Transfer and Gene Duplication of β-Fructofuranosidase Confer Lepidopteran Insects Metabolic Benefits

Horizontal gene transfer (HGT) is a potentially critical source of material for ecological adaptation and the evolution of novel genetic traits. However, reports on posttransfer duplication in organism genomes are lacking, and the evolutionary advantages conferred on the recipient are generally poorly understood. Sucrase plays an important role in insect physiological growth and development. Here, we performed a comprehensive analysis of the evolution of insect β-fructofuranosidase transferred from bacteria via HGT. We found that posttransfer duplications of β-fructofuranosidase were widespread in Lepidoptera and sporadic occurrences of β-fructofuranosidase were found in Coleoptera and Hymenoptera. β-fructofuranosidase genes often undergo modifications, such as gene duplication, differential gene loss, and changes in mutation rates. Lepidopteran β-fructofuranosidase gene (SUC) clusters showed marked divergence in gene expression patterns and enzymatic properties in Bombyx mori (moth) and Papilio xuthus (butterfly). We generated SUC1 mutations in B. mori using CRISPR/Cas9 to thoroughly examine the physiological function of SUC. BmSUC1 mutant larvae were viable but displayed delayed growth and reduced sucrase activities that included susceptibility to the sugar mimic alkaloid found in high concentrations in mulberry. BmSUC1 served as a critical sucrase and supported metabolic homeostasis in the larval midgut and silk gland, suggesting that gene transfer of β-fructofuranosidase enhanced the digestive and metabolic adaptation of lepidopteran insects. These findings highlight not only the universal function of β-fructofuranosidase with a link to the maintenance of carbohydrate metabolism but also an underexplored function in the silk gland. This study expands our knowledge of posttransfer duplication and subsequent functional diversification in the adaptive evolution and lineage-specific adaptation of organisms.