Bacterial nanomachines: the flagellum and type III injectisome

The bacterial flagellum and the virulence-associated injectisome are complex, structurally related nanomachines that bacteria use for locomotion or the translocation of virulence factors into eukaryotic host cells. The assembly of both structures and the transfer of extracellular proteins is mediated by a unique, multicomponent transport apparatus, the type III secretion system. Here, we discuss the significant progress that has been made in recent years in the visualization and functional characterization of many components of the type III secretion system, the structure of the bacterial flagellum, and the injectisome complex.     

The type III secretion injectisome

The type III secretion injectisome is a complex nanomachine that allows bacteria to deliver protein effectors across eukaryotic cellular membranes. In recent years, significant progress has been made in our understanding of its structure, assembly and mode of operation. The principal structural components of the injectisome, from the base located in the bacterial cytosol to the tip of the needle protruding from the cell surface, have been investigated in detail. The structures of several constituent proteins were solved at the atomic level and important insights into the assembly process have been gained. However, despite the ongoing concerted efforts of molecular and structural biologists, the role of many of the constituent components of this nanomachine remain unknown.     

The Spiroplasma heritable bacterial endosymbiont of Drosophila

Since the discovery of the small, gram-positive bacterium, Spiroplasma, as a sex-ratio distorting agent in Drosophila over 50 years ago, substantial progress has been made in understanding the relationship of this bacteria with its insect host. Thus far, spiroplasmas have been found as heritable endosymbionts in sixteen different species of Drosophila. In some species these bacteria cause a male-killing phenotype, where the males die during embryogenesis. In other species, however, Spiroplasma does not cause male-killing, and its fitness effects are unclear. Though recent research has identified multiple factors that affect the prevalence and transmission of spiroplasmas in Drosophila populations, much work remains to fully characterize this symbiosis. Spiroplasma is the only identified heritable bacterial endosymbiont of Drosophila, other than Wolbachia, and can serve as a useful as model for elucidating the nature of insect/bacterial interactions.     

Bacterial secretins: Mechanisms of assembly and membrane targeting

Secretion systems are employed by bacteria to transport macromolecules across membranes without compromising their integrities. Processes including virulence, colonization, and motility are highly dependent on the secretion of effector molecules toward the immediate cellular environment, and in some cases, into the host cytoplasm. In Type II and Type III secretion systems, as well as in Type IV pili, homomultimeric complexes known as secretins form large pores in the outer bacterial membrane, and the localization and assembly of such 1 MDa molecules often relies on pilotins or accessory proteins. Significant progress has been made toward understanding details of interactions between secretins and their partner proteins using approaches ranging from bacterial genetics to cryo electron microscopy. This review provides an overview of the mode of action of pilotins and accessory proteins for T2SS, T3SS, and T4PS secretins, highlighting recent near‐atomic resolution cryo‐EM secretin complex structures and underlining the importance of these interactions for secretin functionality.     

Gene-for-gene interactions: bacterial avirulence proteins specify plant disease resistance

Resistance of plants to bacterial pathogens is often controlled by corresponding genes for resistance and avirulence in host and pathogen, respectively. Fifty years after discovery of the genetic basis of gene-for-gene interactions, several avirulence and plant resistance genes have been isolated and are being studied on the molecular level. Tremendous progress has been made due to a better understanding of type III secretion systems that are required for bacterial pathogenicity. We are beginning to grasp how the plant actually recognizes bacterial avirulence determinants. The current view is that the bacterium translocates avirulence proteins into the host cell by the Hrp type III secretion system and that recognition occurs in the plant cell.     

Iron acquisition by Gram-positive bacterial pathogens

For the majority of bacterial pathogens, acquisition of iron from host proteins is a prerequisite for growth during infection. The mechanisms by which Gram-negative bacteria obtain iron from host proteins have been well described, but only recently has substantial progress been made in identifying these mechanisms for Gram-positive bacterial pathogens. This review provides an overview of the existing knowledge on the genetic basis of iron transport for important Gram-positive pathogens.     

The bacterial outer membrane β-barrel assembly machinery

β-Barrel proteins found in the outer membrane of Gram-negative bacteria serve a variety of cellular functions. Proper folding and assembly of these proteins are essential for the viability of bacteria and can also play an important role in virulence. The β-barrel assembly machinery (BAM) complex, which is responsible for the proper assembly of β-barrels into the outer membrane of Gram-negative bacteria, has been the focus of many recent studies. This review summarizes the significant progress that has been made toward understanding the structure and function of the bacterial BAM complex.     

The type III secretion system tip complex and translocon

The type III secretion machinery of Gram-negative bacteria, also known as the injectisome or needle complex, is composed of a basal body spanning both bacterial membranes and the periplasm, and an external needle protruding from the bacterial surface. A set of three proteins, two hydrophobic and one hydrophilic, are required to allow translocation of proteins from the bacterium to the host cell cytoplasm. These proteins are involved in the formation of a translocation pore, the translocon, in the host cell membrane. Exciting progress has recently been made on the interaction between the translocators and the injectisome needle and the assembly of the translocon in the host cell membrane. As expected, the two hydrophobic translocators insert into the target cell membrane. Unexpectedly, the third, hydrophilic translocator, forms a complex on the distal end of the injectisome needle, the tip complex, and serves as an assembly platform for the two hydrophobic translocators.     

Poisons, ruffles and rockets: bacterial pathogens and the host cell cytoskeleton

The cytoskeleton of eukaryotic cells is affected by a number of bacterial and viral pathogens. In this review we consider three recurring themes of cytoskeletal involvement in bacterial pathogenesis: 1) the effect of bacterial toxins on actin-regulating small GTP-binding proteins; 2) the invasion of non-phagocytic cells by the bacterial induction of ruffles at the plasma membrane; 3) the formation of actin tails and pedestals by intracellular and extracellular bacteria, respectively. Considerable progress has been made recently in the characterization of these processes. It is becoming clear that bacterial pathogens have developed a variety of sophisticated mechanisms for utilizing the complex cytoskeletal system of host cells. These bacterially-induced processes are now providing unique insights into the regulation of fundamental eukaryotic mechanisms.     

Molecular microbiology in antibacterial research

The special issue of Journal of Microbiology contains six reviews dealing with cutting edge research achievements in the fields of molecular microbiology focusing on antibacterial research. In a more specific sense, this special issue helps outline the progress of 21^st-century basic molecular microbiology that can encompass related disciplines regarding a variety of interactions involving bacteria during bacterial pathogenesis and their control: sociomicrobiology (interaction between bacteria), immunology (interaction between bacteria and their hosts), and bacteriophage (phage) virology (interaction between bacteria and their parasites). Recent advancements have rapidly been made in our understanding of the real situation regarding polymicrobial interactions during bacterial infection and in non-mammalian host infection models to uncover the molecular mechanisms of host-bacteria interactions, which will complement our growing knowledge about immune responses toward bacterial and environmental elicitors. Moreover, much attention has recently been paid to phages and phage products as potential antibacterial therapeutics in the era of antibiotic resistance. Below, I summarize the individual contributions in these distinct categories.     

The push and pull of the bacterial cytoskeleton

A crucial function for eukaryotic cytoskeletal filaments is to organize the intracellular space: facilitate communication across the cell and enable the active transport of cellular components. It was assumed for many years that the small size of the bacterial cell eliminates the need for a cytoskeleton, because simple diffusion of proteins is rapid over micron-scale distances. However, in the last decade, cytoskeletal proteins have indeed been found to exist in bacteria where they have an important role in organizing the bacterial cell. Here, we review the progress that has been made towards understanding the mechanisms by which bacterial cytoskeletal proteins influence cellular organization. These discoveries have advanced our understanding of bacterial physiology and provided insight into the evolution of the eukaryotic cytoskeleton.     

Abundance and function of bacteria in the Southern Ocean.

The very low water temperatures existing in polar oceans that experience seasonal advance and retreat of pack ice do not inhibit the presence of large bacterial populations. Bacteria may contribute significantly to the energy transfers within the Southern Ocean. In the last decades, notable progress has been made in the knowledge of the role of marine bacteria in the Southern Ocean. A short overview of the abundance and function ofAntarctic marine bacteria is given, with respect to metabolic activity. The importance of spatial and temporal variability is described. The ecological function of Antarctic marine bacterioplankton is discussed. Depending on food web structure, bacteria may be either a link in food webs supporting metazoan production, or a sink where bacterial production is metabolised by microorganisms. In the more oligotrophic areas and during certain periods of the year bacterial biomass dominates phytoplankton. The microbial food web is therefore the dominant pathway for carbon and energy flow in Antarctic seawater.     

Visualization of harpin secretion in planta during infection of apple seedlings by Erwinia amylovora

Erwinia amylovora is a Gram-negative pathogenic bacterium that infects pear and apple trees as well as other plants from the Rosaceae family. E. amylovora pathogenicity is dependent on a functional Hrp type III secretion system. Harpin, a protein playing a major role in virulence, has been shown to be exported in vitro via the type III secretion apparatus. The data presented here focus on harpin detection in planta after infection of apple seedlings with the wild-type strain CFPB 1430. Using a specific harpin antiserum, harpin was not detected inside the host plant cells, but was found associated with the bacteria and secreted. The extracellular localization of harpin is in agreement with the physiological effects induced by purified harpin when applied as an exogenous elicitor. Harpin was not found associated with the host plant cell wall, a result that weakens its postulated role in cell wall loosening. A differential labelling was observed at the bacterial level: for some bacteria, harpin was exclusively cytoplasmic, whereas in others, it appeared as small patches over the bacterial outer membrane or associated with extracellular linear structures. All the bacteria present within the same area were similarly labelled, suggesting co-ordination in the secretion process. All observations suggest that harpin is synthesized in the bacterial cytoplasm and that secretion occurs from this cytoplasmic pool upon sensing of a plant or bacterial signal.     

Functional characteristics and catalytic mechanisms of the bacterial hyaluronan synthases

The first gene for a glycosaminoglycan synthase to be cloned was the hyaluronan (HA) synthase from S. pyogenes, which we reported in 1993. Since then, at least 20 bacterial, viral, or eukaryotic HA synthase gene or cDNA sequences and two bacterial chondroitin synthase genes have been reported. During the last decade a great deal has been elucidated about the structure, function, and mechanisms of action of the bacterial HA synthases, which are the focus of this review. Very rapid progress has been made in elucidating the mechanism of HA synthesis by the HA synthase from Pasteurella multocida. Although little of this information is applicable to understanding the mechanism of action of streptococcal HA synthases, good progress has also been made in understanding how these latter enzymes work.     

Aquatic Microbiology for Ecosystem Scientists: New and Recycled Paradigms in Ecological Microbiology

In all ecosystems, bacteria are the most numerous organisms and through them flows a large fraction of annual primary production. In the past decade we have learned a great deal about some of the factors that regulate bacteria and their activities, and how these activities, in turn, alter ecosystem-level processes. Here I review three areas in which recent progress has been made with particular reference to pelagic ecosystems: the problem of bacterial cell dormancy; the effect of solar radiation on organic matter lability; and, the maintenance of net heterotrophy. In a system in which grazing is the major source of mortality for bacteria, bacterial cell dormancy is something of a paradox. I argue that the degree to which bacteria are grazed by flagellates (highly selective grazers) versus other grazers (cladocerans, bivalves) may explain the degree and variation in the proportion of active cells which recent evidence shows to be large. Another factor affecting bacterial activity that has come to the fore in recent years is solar radiation. Irradiation, especially in the ultra-violet range has long been thought of as simply deleterious to some bacteria. A wealth of newer evidence shows that refractory dissolved organic compounds may be converted into microbially labile compounds by solar radiation in several wavebands. This interaction between irradiation and organic matter (photolysis) may explain, in part, how dissolved organic carbon (C) may be refractory in the dark environment of the soil but become labile in the illumunated surface waters of lakes or rivers. The newer evidence shows that aquatic ecosystems, at least oligotrophic ones, are significantly subsidized by terrestrially-produced organic matter. I review here multiple lines of evidence that suggest that freshwater ecosystems are predominantly systems which respire more organic C than they produce by photosynthesis, and are therefore net heterotrophic. While net heterotrophy is an interesting exception for terrestrial ecosystems, it appears to be commonplace for aquatic systems and represents an important linkage between terrestrial and aquatic ecosystems.     

大肠杆菌Ⅲ型分泌系统2毒力岛研究进展

许多革兰氏阴性菌借助Ⅲ型分泌系统黏附在宿主细胞表面,然后跨越胞膜将特异性蛋白注入宿主细胞内,破坏宿主细胞内的多种信号通路,从而有利于细菌的感染及定殖。在肠致病性大肠杆菌(Enteropathogenic Escherichia coli,EPEC)中,除了肠细胞脱落位点(Locus of entericyte effacement,LEE)毒力岛编码的Ⅲ型分泌系统(Type Ⅲ secretion system,T3SS)外,在分析肠出血性大肠杆菌O157:H7的基因组序列时发现一个新的Ⅲ型分泌系统,大肠杆菌Ⅲ型分泌系统2(Escherichia coli type Ⅲ secretion system 2,ETT2)毒力岛。研究显示,ETT2可能在大多数菌株中不具有完整的分泌系统功能,但是其对于细菌毒力的发挥具有重要作用。因此,本文简要综述了大肠杆菌ETT2的基因特征、ETT2的分布与流行、ETT2的功能与机制等方面的主要研究进展。     

Regulatory Networks of the T4SS Control: From Host Cell Sensing to the Biogenesis and the Activity during the Infection

Delivery of effectors, DNA or proteins, that hijack host cell processes to the benefit of bacteria is a mechanism widely used by bacterial pathogens. It is achieved by complex effector injection devices, the secretion systems, among which Type 4 Secretion Systems (T4SSs) play a key role in bacterial virulence of numerous animal and plant pathogens. Considerable progress has recently been made in the structure–function analyses of T4SSs. Nevertheless, the signals and processes that trigger machine assembly and activity during infection, as well as those involved in substrate recognition and transfer, are complex and still poorly understood. In this review, we aim at summarizing the last updates of the knowledge on signaling pathways that regulate the biogenesis and the activity of T4SSs in important bacterial pathogens.     

Bacterial genetics: past achievements, present state of the field, and future challenges

Genetic tools are required to take full advantage of the wealth of information generated by genome sequencing efforts and ensuing global gene and protein expression analyses. Bacterial genetics was originally developed and refined in Escherichia coli. As a consequence, elegant plasmid, cloning, expression, and mutagenesis systems were developed over the years and a good number of them are commercially available. This is not true for other bacteria. Although the development of genetic tools has generally not kept up with the sequencing pace, substantial progress has been made in this arena with many bacterial species. This short review highlights selected topics and achievements in the field over the past 25 years and presents some strategies that may help address future challenges. BioTechniques has played an integral part in the publication of important technological advances in the field over the first 25 years of its existence and it can be anticipated that it will continue to do so in the future.     

翻译延伸因子EF-P的结构和功能及其研究进展

EF-P(Elongation factor P)是普遍存在于细菌中的蛋白质翻译延伸因子,因其L型结构与t RNA类似,可挽救聚脯氨酸导致的翻译延宕,减缓核糖体的失速效应。EF-P虽然不是细菌生存的必需蛋白,但是对细菌自身的环境适应性以及一些致病菌的毒性维持至关重要。本文综述了细菌EF-P的结构、功能及其相关研究进展。     

Regulation of bacterial virulence by two-component systems

In bacteria, two-component systems (TCS) are widely used signal transduction devices which are engaged in a multitude of gene regulatory systems that respond to changing growth conditions. Many pathogenic bacteria encounter different microenvironments during their infectious cycle and their ability to efficiently adapt to different niches inside and outside of their host organisms is frequently mediated by TCSs, which can, therefore, be considered as an essential prerequisite for their pathogenicity. Although significant progress has been made in the elucidation of basic principles of the signal transduction process itself, in many pathogens the contribution of TCS to bacterial virulence is insufficiently recognized.