冰核活性细菌基因的研究进展及其应用

冰核活性细菌是一类可以诱导过冷水结冰而导致霜冻灾害的细菌,它已成为一种重要的生物资源获得广泛的研究与开发,在基础理论和应用研究方面取得了较大进展。近些年来,许多国家的学科研究者对于冰核基因的研究与开发开展了大量的工作。自1985年克隆出了第一个冰核基因后,目前已经从冰核细菌中克隆了8个冰蛋白基因并完成了测序。冰核活性细菌及基因资源具有广阔的研究开发的价值,且具有良好的应用前景。所以,对于冰核活性基因的结构特点及近年来的研究现状有个总体了解是很有必要的。本文主要介绍了冰核活性基因及其应用方面的研究进展情况。     

Origin of the bacterial SET domain genes: vertical or horizontal?

The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, be involved in bacteria-host interactions. The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. By phylogenetic analysis, examination of individual chromosomal regions for signs of insertion, and evaluating the chromosomal versus SET domain genes' GC contents, we provide evidence that SET domain genes have existed in the bacterial domain of life independently of eukaryotes. The bacterial genes have undergone an evolution of their own unconnected to the evolution of the eukaryotic SET domain genes. Initial finding of SET domain genes in predominantly pathogenic and symbiotic bacteria resulted, most probably, from a biased sample. However, a lateral transfer of SET domain genes may have occurred between some bacteria and a family of Archaea. A model for the evolution and distribution of SET domain genes in bacteria is proposed.     

Common ancestry of iron oxide- and iron-sulfide-based biomineralization in magnetotactic bacteria

Magnetosomes are prokaryotic organelles produced by magnetotactic bacteria that consist of nanometer-sized magnetite (Fe₃O₄) or/and greigite (Fe₃S₄) magnetic crystals enveloped by a lipid bilayer membrane. In magnetite-producing magnetotactic bacteria, proteins present in the magnetosome membrane modulate biomineralization of the magnetite crystal. In these microorganisms, genes that encode for magnetosome membrane proteins as well as genes involved in the construction of the magnetite magnetosome chain, the mam and mms genes, are organized within a genomic island. However, partially because there are presently no greigite-producing magnetotactic bacteria in pure culture, little is known regarding the greigite biomineralization process in these organisms including whether similar genes are involved in the process. Here using culture-independent techniques, we now show that mam genes involved in the production of magnetite magnetosomes are also present in greigite-producing magnetotactic bacteria. This finding suggest that the biomineralization of magnetite and greigite did not have evolve independently (that is, magnetotaxis is polyphyletic) as once suggested. Instead, results presented here are consistent with a model in which the ability to biomineralize magnetosomes and the possession of the mam genes was acquired by bacteria from a common ancestor, that is, the magnetotactic trait is monophyletic.     

Phylogeny of nitrite reductase (nirK) and nitric oxide reductase (norB) genes from Nitrosospira species isolated from soil

Ammonia-oxidizing bacteria are believed to be an important source of the climatically important trace gas nitrous oxide (N(2)O). The genes for nitrite reductase (nirK) and nitric oxide reductase (norB), putatively responsible for nitrous oxide production, have been identified in several ammonia-oxidizing bacteria, but not in Nitrosospira strains that may dominate ammonia-oxidizing communities in soil. In this study, sequences from nirK and norB genes were detected in several cultured Nitrosospira species and the diversity and phylogeny of these genes were compared with those in other ammoniaoxidizing bacteria and in classical denitrifiers. The nirK and norB gene sequences obtained from Nitrosospira spp. were diverse and appeared to be less conserved than 16S rRNA genes and functional ammonia monooxygenase (amoA) genes. The nirK and norB genes from some Nitrosospira spp. were not phylogenetically distinct from those of denitrifiers, and phylogenetic analysis suggests that the nirK and norB genes in ammonia-oxidizing bacteria have been subject to lateral transfer.     

高效柴油降解菌Acinetobacter sp.W3分离鉴定及降解酶基因扩增分析

从柴油污染的海水样品中分离高效柴油降解细菌,分析菌株对柴油的降解能力及降解酶基因,为海洋柴油污染的生物修复奠定基础。选取浙江定海港柴油污染的海水样品,进行降解菌的富集培养;采用常规方法分离筛选高效柴油降解菌。利用革兰氏染色、形态学观察、生理生化鉴定及16S rDNA分析等方法对降解菌株进行种属鉴定。采用紫外吸收法测定菌株对柴油的降解率。采用PCR方法、核酸序列测定和比对,对其降解酶基因进行扩增分析。筛选出一株高效降解菌,形态学观察及生理生化鉴定初步确定为不动杆菌。16S rDNA序列分析及比对结果表明,其16S rDNA序列与威尼斯不动杆菌(Acinetobacter venetianus)属的序列同源性达到99.7%,命名为不动杆菌W3(Acinetobactersp.W3),该菌对柴油的7 d降解率达到84.7%。PCR方法从Acinetobactersp.W3菌株中的基因组DNA和质粒DNA上扩增到了大小为540 bp的烷烃羟化酶基因alkB和864 bp的CYP153A部分DNA片段,分别与Acinetobacter venetianus1-D-2的alkB和Acinetobactersp.OC4、Acinetobactersp.EB104的CYP153具有99%和98%的同源性。从定海港口柴油污染海水分离得到一株高效柴油降解菌Acinetobactersp.W3,该菌属于不动杆菌属,含有烷烃降解酶基因,能高效降解柴油污染物,有望应用于海水柴油污染的生物修复。     

基因芯片技术在病原细菌检测中的应用

基因芯片技术具有快速、高通量、平行化等优点,在病原细菌检测中有广泛的应用前景,选择细菌适宜的靶基因是芯片制备的关键之一。用细菌核糖体基因做靶基因的芯片技术,虽然应用广泛,但仍存在一些不足,随着基因组信息及基因功能的深入研究,包括毒力基因、耐药基因等具有较好种属特异性的细菌基因不断被发现,为芯片技术检测病原细菌提供了更多特异的靶基因,使检测结果更加灵敏、准确,在病原细菌研究中将发挥更大的作用。     

铁氧化菌耐砷机制及其砷污染修复应用的研究进展

砷污染作为全球性环境问题已经引起了人们的高度重视。无机砷化合物可与铁氢氧化物络合通过共沉淀作用去除。因此,利用具有砷耐性的铁氧化菌氧化环境中的铁元素去除砷化合物具有潜在的应用前景。目前已有利用铁氧化菌去除环境中砷污染物的报道。用于砷污染修复的铁氧化菌必须有一定的砷耐性才能在含砷环境中行使功能。微生物是否具有砷耐性往往取决于基因,并且不同的菌株具有不同的生理特征,适宜不同砷污染环境的修复。本文通过对8株代表性的铁氧化菌砷耐性基因的总结,阐述其耐砷机制、研究概况及应用前景,以期为铁氧化菌用于除砷新技术的开发提供参考。     

食品级乳酸菌表达系统研究进展

乳酸菌表达系统是近几年发展起来的食品级高效表达系统。乳酸菌具有益生菌特征,因此该表达系统与其他细菌表达系统相比有很多优点。介绍了糖诱导表达系统、噬菌体Φ31爆发式诱导的表达系统、乳链球菌素调控表达系统、温控表达系统等的研究进展,以及这些系统的应用前景。     

插入序列共同区元件：细菌中新出现的一种基因捕获系统

摘要：插入序列共同区（Insertion sequence common region,ISCR）元件是一类在结构和功能上与IS91家族相似的特殊插入序列,特点是缺少了末端反向重复序列（Inverted repeats, IRs）,在插入位点不产生直接重复序列,并通过滚环式（Rolling circle, RC）进行转座。ISCR元件作为一种新的基因捕获系统,它可以移动邻近的任何DNA序列,为耐药基因在不同种属细菌间水平传播提供了高效的媒介。世界各地多种革兰氏阴性病原菌中已发现有19种ISCR元件,大部分ISCR元件同时携带了多种耐药基因,提示ISCR有可能会造成细菌多重耐药性的快速传播。本文就ISCR结构特征、类型、移动方式、起源及进化的研究进展进行了综述。     

细菌在实体肿瘤治疗中的应用

150多年前就发现某些细菌能够选择性地在实体肿瘤部位生长聚集,而在正常组织器官则否。尽管对产生这一现象的原因尚不明了,但人们已经利用细菌的这一特性,就试图将其作为治疗实体肿瘤的一种非常有前景的方法进行了研究。随着基因工程技术的日益完善,以及新的具有肿瘤靶向性细菌的发现,细菌作为肿瘤靶向性载体用于治疗肿瘤已日益受到青睐。这些细菌被用来传递抗肿瘤生长或杀伤肿瘤的物质,如毒素、前药转化酶、血管生长抑制剂、细胞因子等。     

Evidences of lateral gene transfer between archaea and pathogenic bacteria

Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism’s biology and may play a role in pathogenesis.     

The molecular biology of barophilic bacteria

Many microorganisms from the deep-sea display high-pressure-adapted — also described as barophilic or piezophilic — growth characteristics. Phylogenetic studies have revealed that a large proportion of the barophilic bacteria currently in culture collections belong to a distinct subgroup of the genus Shewanella, referred to as the “barophile branch.“ Many of the basic properties of barophiles that enable their survival at extremes of pressure remain to be elucidated. However, several genes whose expression is regulated by pressure, or which appear to be critical to baroadaptation, have been uncovered. One such operon, whose presence appears to be restricted to the “barophile branch,” has been identifed in DNA samples obtained from sediments recovered in the deepest ocean trench. In the case of another set of pressure-regulated genes, regulatory elements required for pressure signaling have been uncovered. The nature and regulation of these genes is discussed. Received: February 19, 1997 / Accepted: March 3, 1997     

乳酸菌食品级表达载体的研究与应用

乳酸菌是能够发酵糖类产生大量有机酸的革兰氏阳性菌的通称,在发酵食品中有着悠久的应用历史.乳酸菌通常被认为是安全菌株,这些微生物的基因工程操作在食品、医学等方面具有广阔的应用前景.表达载体是基因工程中常用的工具之一,大多数乳酸菌的表达载体通常以抗生素抗性基因作为选择标记,然而抗性基因具有潜在的转移性,因此需要开发食品级表...     

Microbial diversity in the Bassin d’Arcachon coastal lagoon (SW France)

The high biodiversity observed in coastal lagoons can often be related to a very high degree of environmental heterogeneity (β-biodiversity). In this article, I describe many physical factors that contribute to create environmental heterogeneity and different habitats within the Bassin d’Arcachon, a mesotidal lagoon in S.W. France. The microbial biodiversity has been studied in this coastal lagoon by culture-dependent and culture-independent techniques. The sediments of the meadows of the seagrass Zostera noltii have received a specific focus. During the last 15 years, several novel bacterial species have been isolated from these sediments and obtained in culture. Among these, five different species have been fully described as novel species according the Bacteriological Code and two of them represent also the type strain for a novel genus. The bacterial biodiversity has also been studied by molecular ecology techniques. An early study was focused on water column bacteria and a comparison has been made with the same community from the more eutrophic Prévost lagoon (France, Mediterranean coast). A clone library was also constructed for 16-S rRNA genes isolated and amplified from the 1–2 cm depth layer of the Z. noltii sediment. These studies showed a high degree of biodiversity and the importance of sulfate-reducing bacteria in the sediment, pointing to species that have not been obtained in culture. Collectively, these data show that there is still a large discrepancy between culture-dependent and culture-independent prokaryotic biodiversity. It is important to link the functional biogeochemical approach with the biodiversity approach. For the Bassin d’Arcachon studies, the biogeochemical approach has successfully nurtured the biodiversity studies, while the reverse has not yet been the case as the biogeochemical studies have lumped prokaryotes in functional groups. Guest editors: A. Razinkovas, Z. R. Gasiūnaitė, J. M. Zaldivar & P. Viaroli European Lagoons and their Watersheds: Function and Biodiversity     

Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China

Aims:  Shanyin County is one of the most severe endemic arsenism affected areas in China but micro-organisms that potentially release arsenic from sediments to groundwater have not been studied. Our aim was to identify bacteria with the potential to metabolize or transform arsenic in the sediments.
Methods and Results:  Culture and nonculture-based molecular methods were performed to identify arsenite-oxidizing bacteria, arsenate-reducing bacteria and arsenite oxidase genes. Arsenite-oxidizing bacteria were identified only from the land surface to 7 m underground that were affiliated to α- and β-Proteobacteria. Arsenate-reducing bacteria were found in almost all the sediment samples with different depths (0–41 m) and mainly belong to γ-Proteobacteria. Several novel arsenite oxidase genes ( aoxBs ) were identified from the upper layers of the sediments (0–7 m) and were found to be specific for arsenite-oxidizing bacteria.
Conclusions:  The distribution of arsenite-oxidizing bacteria in upper layers and arsenate-reducing bacteria in different depths of the sediments may impact the arsenic release into the nearby tubewell groundwater.
Significance and Impact of the Study:  This study provides valuable sources of micro-organisms (and genes) that may contribute to groundwater arsenic abnormality and may be useful to clean arsenic contaminated groundwater.     

微塑料附着微生物研究进展

近年来,微塑料引起的环境污染已经成为一个全球性的问题,在海洋环境中,微生物可以附着于微塑料表面形成生物被膜。已有研究表明生物被膜可以为生活在其内部的细菌提供保护,被膜中可能富集了对人体或者水生生物有害的致病菌,且频繁的基因交流可能产生更多耐药菌。微塑料表面附着的微生物,能借助大洋环流随微塑料在海洋中迁徙,进而可能引起微生物入侵事件的发生。主要对微塑料与生物被膜之间的相互作用、微塑料与附着在其表面的塑料降解菌、微塑料与致病菌、微塑料对微生物迁徙的影响,以及微塑料表面生物被膜中耐药基因的扩散进行综述,对微塑料附着微生物未来研究方向进行了展望,为更好地了解海洋微塑料污染提供参考。     

乳酸菌食品级基因表达系统

酸菌是一类重要工业菌株。最近,乳酸菌遗传学和分子生物学的研究取得长足进步,导致发展了乳酸菌食品级基因表达系统。通过介绍乳酸菌食品级基因表达系统的基本要求、食品级选择性标记、食品级诱导物及该系统的研究进展,展示了乳酸菌食品级基因表达系统的建立对研究乳酸菌的基因表达调控和它的深层次的开发利用所具有的重要意义。     

Enumeration and characterization of culturable arsenate resistant bacteria in a large estuary

Arsenic is a toxic element that exists in two major inorganic forms, arsenate and arsenite. A number of bacteria have been shown to resist arsenic exposure, and even more bacteria appear to possess the genes for arsenic resistance. In this study, the numbers of culturable arsenate-resistant bacteria present in water at three coastal sites in the Lake Pontchartrain estuary, Louisiana, was determined. Despite insignificant (less than 1.33 μM) levels of arsenic in this system, 20–50% of the viable count of bacteria showed appreciable arsenate resistance, suggesting that arsenic-resistant bacteria are common and widespread. A diverse array of arsenate-resistant isolates was obtained, with 16S rRNA sequence analysis indicating 37 different bacterial strains, representing six major bacterial groups. Many of these isolates were affiliated with groups of bacteria that have been poorly characterized in terms of arsenic resistance, such as the Betaproteobacteria or Flavobacteria. Some isolates were capable of tolerating very high (>100 mM) levels of arsenate, although arsenite resistance was generally much lower. The results suggest that arsenic-resistant bacteria are common, even in environments with insignificant arsenic contamination, and that many different groups of aquatic bacteria show appreciable arsenic resistance.     

First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA

Nitrite oxidoreductase (NXR) is the key enzyme responsible for the oxidation of NO(2)(-) to NO(3)(-) in nitrite-oxidizing bacteria. For the first time a molecular approach for targeting the nxrA gene was developed, encoding the catalytic subunit of the NXR, to study diversity of Nitrobacter-like organisms based on the phylogeny of nxrA gene sequences in soils. NxrA sequences of the Nitrobacter strains analysed (Nitrobacter hamburgensis, Nitrobacter vulgaris, Nitrobacter winogradskyi, Nitrobacter alkalicus) by PCR, cloning and sequencing revealed the occurrence of multiple copies of nxrA genes in these strains. The copy number and similarity varied among strains. The diversity of Nitrobacter-like nxrA sequences was explored in three soils (a French permanent pasture soil, a French fallow soil, and an African savannah soil) using a cloning and sequencing approach. Most nxrA sequences found in these soils (84%) differed from nxrA sequences obtained from Nitrobacter strains. Moreover, the phylogenetic distribution and richness of nxrA-like sequences was extremely variable depending on soil type. This nxrA tool extends the panel of functional genes available for studying bacteria involved in the nitrogen cycle.