微生物对水环境污染物的趋化性研究进展

随着人类活动的干扰以及社会工业化进程的加剧,水环境污染现象日益严峻。微生物是水环境污染治理和修复的主要驱动者。越来越多的研究发现,水环境中污染物的去除速率与微生物的趋化功能密切相关。综述了近几年有关微生物对水环境中无机盐、溶解性有机物和重金属等的趋化特性研究进展,讨论并展望了基于趋化功能微生物精准调控的水环境污染强化治理技术的应用前景及主要问题。     

环境中污染物降解基因的水平转移(HGT)及其在生物修复中的作用

水平基因转移是不同于垂直基因转移的遗传物质的交流方式.在污染环境这一特异生态环境中,降解基因的水平转移有着独特的功能与作用.研究环境中污染物降解基因在微生物间的水平转移,更深入地了解微生物种群适应污染环境的机理,对于评价污染物的环境毒理、生物可降解性以及污染环境的可修复潜力具有重要参考价值.在污染物生物修复实践中,可以通过调控降解基因的水平转移,增强污染环境中微生物的降解能力,更有效地发挥生物修复作用.文章将对环境中细菌间基因交流的机制,污染物降解基因的水平转移对微生物适应污染环境的机理、水平基因转移对代谢途径的进化及其对污染物生物修复作用的影响等方面的研究进展做一综述.     

土壤与水体有机污染的生物修复及其应用研究进展

系统论述了土壤、水有机污染物的主要来源、特点、有机污染生物修复的概念、应用范围、成功实例与研究进展等,特别是对于泄漏石油污染的生物成功降解方法、效果,土壤中易爆炸物如ＴＮＴ、废水中有机污染的有效降解等,评价了生物修复所具有突出优势,对有机、无机污染物降解过程中植物、微生物筛选、基因修饰、分子克隆与转基因植物方面近年来所取得的惊人成果与突破性进展,无疑正激励着人们开拓更大的应用范围。预计不久的将来,更多具有环境净化与生物修复功能的商业性综合技术与高效性工程生物将投入应用。     

运动细菌的趋化性及其对微生物群落的影响

细菌趋化性是指利用自身的运动能力对环境中化学物质浓度梯度产生响应,使其由随机运动转变为具有偏向性的运动,是细菌适应环境的一种基本属性。了解细菌趋化性及其与环境和微生物体系的相互作用机制,对于阐明它们在调节微生物群落结构、降解污染物和参与生态圈物质循环等方面的作用和影响具有重要意义。本文概述了细菌的常见运动方式、趋化模式和相关信号传导机制;分析探讨了研究细菌趋化性的常见方法及影响细菌趋化性的物理、化学和生物因素;系统阐述了运动细菌的趋化性对微生物群落形成和结构的影响,为研究运动细菌在共生体系或食品发酵过程影响微生物群落结构、菌间互作和物质代谢等方面提供了理论参考。     

微生物对拟除虫菊酯类农药残留的生物修复

拟除虫菊酯类农药是一类高效、广谱农药,且具有低毒性和能被生物降解之特性,但其残留却给人们的健康带来了巨大的威胁,如何有效地去除其残留成为摆在环境工作者面前的一项重大课题。以生物修复为理论基础的农药残留降解菌技术为解决这一难题带来了新思路,该方法操作简便、经济实用,在国内外均成为环境工作者的研究热点。     

生物修复中细菌的遗传修饰

有机污染的土壤过去常用物理修复或化学修复 ,成本较高 ,易引起二次污染 ,还可能危害微生物区系和动物区系。生物修复技术以其独到的优势迅速兴起。土壤中“ＭａｇｉｃＳｉｘ”(水分、氧气、氧化还原电势、ｐＨ值、营养状态、温度 )对微生物降解的影响[1] 或者土著菌 (ｉｎｄｉｇｅｎｏｕｓｂａｃｔｅｒｉａ)缺少编码某一降解酶基因成为污染物生物降解的限制因子 ,土著菌常常难以适应处理环境 ,达不到环境治理工程的目的。细菌对有机污染物适应性的遗传机制研究表明 ,细菌为了在污染地区环境中生存 ,细菌之间可发生水平基因转移或细菌的染色…     

细菌的锌抗性基因及其在生物修复中的应用

随着工业时代的发展,人源性排放已成为环境锌污染的主要来源.这不但破坏了生态系统的稳定,更经食物链富集,对人类健康造成严重威胁.利用含锌抗性基因的(重组)细菌等进行锌治理是生物修复的途径之一.阐述了细菌锌抗性基因的结构、表达产物和一些相关的作用机制,展望其在生物修复方面的应用.     

微生物的运动性和趋化性在共生体系中的作用

许多共生关系依赖于宿主从环境中募集微生物相互作用后形成,而共生微生物的发现和定殖宿主的机制尚不清楚。通常认为环境共生体的获得往往需要运动和趋化作用来使微生物主动迁移和定殖。这些行为在建立和维持共生相互作用方面的关键性已经在少数模式系统中得到了很好地确立和证实。但在大多数环境共生体中,这些行为在很大程度上仍被忽视了。基于对模式案例的分析,总结了宿主应用共生微生物的趋化性和运动性在何时、何地、如何实现共生募集以及有哪些影响募集的因素。强调了这些共生行为在大范围的宿主和环境中的重要性,并对共生关系中微生物的运动性和趋化性的作用研究进行了展望,旨在为今后的相关研究和实际应用提供参考。     

乳酸菌对重金属污染的生物修复作用

乳酸菌具有吸附及积累重金属离子的特性,且乳酸菌对重金属污染的生物修复作用的安全性较高。本研究综述了乳酸菌修复重金属污染的机制,及乳酸菌生物修复重金属污染水体、农产品及生物体的研究现状,为重金属污染的修复提供新思路。乳酸菌作为自然环境中普遍存在的一种安全且可食用微生物,其在生物修复重金属污染方面将发挥其独有的优势。     

铁、锰等金属元素的微生物还原及其在环境生物修复中的意义

讨论了土壤及水体环境中Fe、Mn、U、Se等金属元素的还原,并对还原不同金属的微生物及其对各金属的酶促和非酶促还原机制进行了综述,同时就不同微生物还原各金属在治理环境污染方面的意义进行了概述。     

Association and dissociation kinetics for CheY interacting with the P2 domain of CheA

The chemotaxis system of Escherichia coli makes use of an extended two-component sensory response pathway in which CheA, an autophosphorylating protein histidine kinase (PHK) rapidly passes its phosphoryl group to CheY, a phospho-accepting response regulator protein (RR). The CheA-->CheY phospho-transfer reaction is 100-1000 times faster than the His-->Asp phospho-relays that operate in other (non-chemotaxis) two-component regulatory systems, suggesting that CheA and CheY have unique features that enhance His-->Asp phospho-transfer kinetics. One such feature could be the P2 domain of CheA. P2 encompasses a binding site for CheY, but an analogous RR-binding domain is not found in other PHKs. In previous work, we removed P2 from CheA, and this decreased the catalytic efficiency of CheA-->CheY phospho-transfer by a factor of 50-100. Here we examined the kinetics of the binding interactions between CheY and P2. The rapid association reaction (k(assn) approximately 10(8)M(-1)s(-1) at 25 degrees C and micro=0.03 M) exhibited a simple first-order dependence on P2 concentration and appeared to be largely diffusion-limited. Ionic strength (micro) had a moderate effect on k(assn) in a manner predictable based on the calculated electrostatic interaction energy of the protein binding surfaces and the expected Debye-Hückel shielding. The speed of binding reflects, in part, electrostatic interactions, but there is also an important contribution from the inherent plasticity of the complex and the resulting flexibility that this allows during the process of complex formation. Our results support the idea that the P2 domain of CheA contributes to the overall speed of phospho-transfer by promoting rapid association between CheY and CheA. However, this alone does not account for the ability of the chemotaxis system to operate much more rapidly than other two-component systems: k(cat) differences indicate that CheA and CheY also achieve the chemical events of phospho-transfer more rapidly than do PHK-RR pairs of slower systems.     

Stochastic control of spontaneous signal generation for gradient sensing in chemotaxis

Chemotaxis is characterized by spontaneous cellular behavior. This spontaneity results, in part, from the stochasticity of intracellular reactions. Spontaneous and random migration of chemotactic cells is regulated by spontaneously generated signals, namely transient local increases in the level of phosphoinositol-3,4,5-triphosphate (PIP3 pulses). In this study, we attempted to elucidate the mechanisms that generate these PIP3 pulses and how the pulses contribute to gradient sensing during chemotaxis. To this end, we constructed a simple biophysical model of intracellular signal transduction consisting of an inositol phospholipid signaling pathway and small GTPases. Our theoretical analysis revealed that an excitable system can emerge from the non-linear dynamics of the model, and that stochastic reactions allow the system to spontaneously become excited, which was corresponded to the PIP3 pulses. Based on these results, we framed a hypothesis of the gradient sensing; a chemical gradient spatially modifies a potential barrier for excitation and then PIP3 pulses are preferentially generated on the side of the cell exposed to the higher chemical concentration. We then validated our hypothesis using stochastic simulations of the signal transduction.     

Frozen dynamic dimer model for transmembrane signaling in bacterial chemotaxis receptors.

The crystal structures of the ligand binding domain of a bacterial aspartate receptor suggest a simple mechanism for transmembrane signaling by the dimer of the receptor. On ligand binding, one domain rotates with respect to the other, and this rotational motion is proposed to be transmitted through the membrane to the cytoplasmic domains of the receptor.     

Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis

In chemotaxis of Escherichia coli and other bacteria, extracellular stimuli are perceived by transmembrane receptors that bind their ligands either directly, or indirectly through periplasmic‐binding proteins (BPs). As BPs are also involved in ligand uptake, they provide a link between chemotaxis and nutrient utilization by cells. However, signalling by indirectly binding ligands remains much less understood than signalling by directly binding ligands. Here, we compared intracellular responses mediated by both types of ligands and developed a new mathematical model for signalling by indirectly binding ligands. We show that indirect binding allows cells to better control sensitivity to specific ligands in response to their nutrient environment and to coordinate chemotaxis with ligand transport, but at the cost of the dynamic range being much narrower than for directly binding ligands. We further demonstrate that signal integration by the chemosensory complexes does not depend on the type of ligand. Overall, our data suggest that the distinction between signalling by directly and indirectly binding ligands is more physiologically important than the traditional distinction between high‐ and low‐abundance receptors.     

Antigen‐responsive regulation of Cell motility and migration via the signalobodies based on c‐Fms and c‐Mpl

Since cell migration plays critical roles in development and homeostasis of the body, artificial control of cell migration would be promising for the treatment of various diseases related to migration. To this end, we previously developed single‐chain Fv (scFv)/receptor chimeras, named signalobodies, which can control cell fates via a specific antigen that is different from natural cytokines. Although a conventional chemotaxis chamber assay revealed that several signalobodies based on receptor tyrosine kinases transduced antigen‐dependent migration signals, we have never performed direct observation of the cells to obtain more information on overall properties of cell motility and migration. In this study, we utilized murine pro‐B Ba/F3 cells expressing either a scFv‐Fms or scFv‐Mpl signalobody, and compared their migratory characteristics. We employed a lipid–polyethylene glycol conjugate to softly immobilize the suspension cells on a slide, which facilitated direct observation of chemokinetic activity of the cells. Consequently, both cells markedly exhibited chemokinesis in response to a specific antigen. In addition, the cells were subjected to a stable antigen‐concentration gradient to observe horizontal directional cell migration in real time. The results showed that the cells expressing scFv‐Fms underwent directional migration toward a positive antigen‐concentration gradient. Taken together, we successfully demonstrated antigen‐responsive regulation of cell motility and migration via the signalobodies. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:411–417, 2014     

Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway

Protein–protein interactions play key roles in virtually all cellular processes, often forming complex regulatory networks. A powerful tool to study interactions in vivo is fluorescence resonance energy transfer (FRET), which is based on the distance‐dependent energy transfer from an excited donor to an acceptor fluorophore. Here, we used FRET to systematically map all protein interactions in the chemotaxis signaling pathway in Escherichia coli, one of the most studied models of signal transduction, and to determine stimulation‐induced changes in the pathway. Our FRET analysis identified 19 positive FRET pairs out of the 28 possible protein combinations, with 9 pairs being responsive to chemotactic stimulation. Six stimulation‐dependent and five stimulation‐independent interactions were direct, whereas other interactions were apparently mediated by scaffolding proteins. Characterization of stimulation‐induced responses revealed an additional regulation through activity dependence of interactions involving the adaptation enzyme CheB, and showed complex rearrangement of chemosensory receptors. Our study illustrates how FRET can be efficiently employed to study dynamic protein networks in vivo.     

An allosteric model for transmembrane signaling in bacterial chemotaxis

Bacteria are able to sense chemical gradients over a wide range of concentrations. However, calculations based on the known number of receptors do not predict such a range unless receptors interact with one another in a cooperative manner. A number of recent experiments support the notion that this remarkable sensitivity in chemotaxis is mediated by localized interactions or crosstalk between neighboring receptors. A number of simple, elegant models have proposed mechanisms for signal integration within receptor clusters. What is a lacking is a model, based on known molecular mechanisms and our accumulated knowledge of chemotaxis, that integrates data from multiple, heterogeneous sources. To address this question, we propose an allosteric mechanism for transmembrane signaling in bacterial chemotaxis based on the "trimer of dimers" model, where three receptor dimers form a stable complex with CheW and CheA. The mechanism is used to integrate a diverse set of experimental data in a consistent framework. The main predictions are: (1) trimers of receptor dimers form the building blocks for the signaling complexes; (2) receptor methylation increases the stability of the active state and retards the inhibition arising from ligand-bound receptors within the signaling complex; (3) trimer of dimer receptor complexes aggregate into clusters through their mutual interactions with CheA and CheW; (4) cooperativity arises from neighboring interaction within these clusters; and (5) cluster size is determined by the concentration of receptors, CheA, and CheW. The model is able to explain a number of seemingly contradictory experiments in a consistent manner and, in the process, explain how bacteria are able to sense chemical gradients over a wide range of concentrations by demonstrating how signals are integrated within the signaling complex.