A bacterial actin unites to divide bacterial cells

EMBO J 31 10, 2249–2260 (2012); published online March302012Once thought to exist only in eukaryotic cells, the highly conserved bacterial cytoskeleton is now known to function analogously to its eukaryotic counterparts, particularly in cell shape and division. For instance, the actin-like MreB protein and its homologs are important to maintain cell shape in many rod-shaped bacteria, probably by organizing how peptidoglycan is synthesized. FtsZ, a tubulin homolog, forms a scaffold for the cytokinetic ring, or divisome, by GTP-dependent polymerization into protofilaments. In this issue of The EMBO Journal, Szwedziak et al (2012) reveal the first crystal structures of cell division protein FtsA polymerizing into actin-like filaments, along with in vivo evidence that this self-interaction is crucial for proper cell division.FtsA is an actin homolog required for cytokinesis in many bacterial species and has several key roles in cell division, including helping to tether FtsZ to the cytoplasmic membrane via a membrane-targeting sequence (MTS), recruiting other essential proteins to the divisome, and perhaps promoting divisome constriction (de Boer, 2010). Szwedziak et al (2012) recapitulate the FtsZ-FtsA-membrane association in vitro using liposomes with FtsZ and FtsA proteins from Thermotoga maritima. To get a closer look at the FtsA-FtsZ interface, the authors co-crystallize FtsA with the carboxy-terminal tail of FtsZ, which is known to interact with FtsA. Intriguingly, the crystal reveals an FtsA homodimer. Contrary to the previous bioinformatics model of FtsA self-interaction that proposed a 180° rotation between the two subunits (Carettoni et al, 2003), the FtsA-FtsA interface in the crystal structure shows no rotation, similar to F-actin. Szwedziak et al (2012) also show that FtsA can form longer, actin-like polymers in the presence of non-hydrolysable ATP or on lipid monolayers. These results are surprising because FtsA has a divergent subdomain architecture compared to other actin-family proteins (van den Ent and Löwe).A critical question now is whether FtsA needs to form polymers in vivo to function properly. Purified Streptococcus pneumoniae FtsA assembles into large polymers that are not like F-actin, and it remains unclear if these structures are relevant in vivo (Krupka et al, 2012). Wild-type FtsA proteins do not form detectable filaments in cells, but C-terminal truncations of FtsA that remove the MTS form polymers quite readily in cells when overproduced, although they are not functional (Pichoff and Lutkenhaus, 2007). Even so, starting with an MTS truncation derivative of FtsA to visualize in vivo polymers, Szwedziak et al (2012) design site-directed mutants of Bacillus subtilis FtsA based on the FtsA-FtsA interface of their crystals; these fail to assemble into polymers in vivo. Using a similar MTS truncation derivative, Pichoff et al (2012) created random mutations in Escherichia coli FtsA, and found that those mapping to the same interface found by Szwedziak et al (2012) also disrupted polymer formation. Together, these data suggest that these residues are needed for FtsA self-interaction. Perplexingly, when these mutants were subsequently tested for functionality in the context of full-length FtsA, the results were mixed. Pichoff et al (2012) showed that FtsA mutants deficient for self-interaction in E. coli have a gain-of-function phenotype, whereas Szwedziak et al (2012) report that analogous mutants in B. subtilis FtsA suffer a loss of function. These results support the idea that FtsA self-association is related to its activity (Shiomi and Margolin, 2007), yet understanding how self-interaction regulates FtsA function clearly requires further study.The ability of eukaryotic cytoskeletal proteins to form long polymers is essential to their function, but the physiological relevance of long polymer formation by bacterial cytoskeletal proteins is now a topic of debate (Figure 1). For example, it has been hypothesized that FtsZ protofilaments wrap around the entire circumference of the cell to form the cytokinetic ring. However, recent studies using photoactivated localization microscopy (PALM) and electron cryotomography reveal a different model in which FtsZ forms a series of very short polymers that overlap to encompass the diameter of the cell (Li et al, 2007; Fu et al, 2010). MreB was also originally thought to form long-range helical polymers extending the length of the cell, but recent data obtained with more sophisticated microscopic techniques suggest that MreB is distributed in patches that move circumferentially and independently (White and Gober, 2012). It is not yet clear which of these models represents the true cellular architecture of MreB, although it is likely that some degree of MreB polymerization is still needed for function. It is notable that other bacterial homologs of actin and tubulin used for generating scaffolds or partitioning plasmid DNA, but not for essential cellular processes such as cell division and growth, tend to form long polymers that extend throughout the cell (Pogliano, 2008). The continued combined use of microscopic, biochemical, and genetic methods, as demonstrated by Szwedziak et al (2012) will enhance future understanding of ancestral tubulin and actin proteins in prokaryotes.Open in a separate windowFigure 1Bacterial actin and tubulin filaments involved in cell growth and division. (A) MreB (purple) has long been thought of as a spiral filament twisting along the cell length to control cell shape. Likewise, FtsZ protofilaments (blue) were once thought to wrap around the cell midpoint to organize the divisome. (B) Recent work using high-resolution microscopy has revealed that long cytoskeletal filaments are more likely to be short patches of polymers. The present work by Szwedziak et al (2012) has added FtsA actin-like filaments (green) to the model of possible divisome architecture.     

细菌性阴道病的细菌因素研究进展

细菌性阴道病是妇科常见疾病,对女性、胎儿和新生儿的健康构成严重威胁.阴道微生物群落中产H2O2的乳酸杆菌与厌氧菌数量发生转换为其主要特征,具体机制不清.本文系统综述了近年来细菌性阴道病的细菌因素研究进展.     

On bacterial dissociation

A possible explanation for bacterial dissociation is presented. Alternation of haploidy to diploidy to haploidy is offered as an explanation for dissociation. By studying dissociation with such an approach, the real sexual mechanism of bacteria may be discovered.     

The bacterial cytoskeleton

Bacteria contain a complex cytoskeleton that is more diverse than previously thought. Recent research provides insight into how bacterial actins, tubulins, and ParA proteins participate in a variety of cellular processes.     

Deciphering the bacterial glycocode: recent advances in bacterial glycoproteomics

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Highlights► Bacterial glycoproteins are potential drug targets and are worthy of study. ► Metabolic glycan labeling enables discovery and characterization of glycoproteins. ► Lectin arrays permit monitoring of bacterial glycoprotein dynamics. ► Crosslinking sugars reveal binding partners of glycoproteins to elucidate function. ► Bacterial glycosylation systems facilitate efficient glycoprotein production.     

Contribution of bacterial outer membrane vesicles to innate bacterial defense

Background

Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL) in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the genera Aspergillus and Penicillium and from some pathogens such as Colletotrichum gloeosporioides. The organism used in the present study, Colletotrichum lindemuthianum, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host, Phaseolus vulgaris. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively.

Results

Here we report the isolation and sequence analysis of the Clpnl2 gene, which encodes the pectin lyase 2 of C. lindemuthianum, and its expression in pathogenic and non-pathogenic races of C. lindemuthianum grown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase from C. gloeosporioides.

Conclusions

The Clpnl2 gene of C. lindemuthianum shares the characteristic elements of genes coding for pectin lyases. A time-course analysis revealed significant differences between the two fungal races in terms of the expression of Clpnl2 encoding for pectin lyase 2. According to the results, pectin lyases from bacteria and fungi separated early during evolution. Likewise, the enzymes from fungi and oomycetes diverged in accordance with their differing lifestyles. It is possible that the diversity and nature of the assimilatory carbon substrates processed by these organisms played a determinant role in this phenomenon.     

Simulated bacterial growth

A mathematical model system for the simulation of bacterial growth is presented, based on eight observable growth parameters used as input. These parameters reflect the chain elongation rates of DNA, RNA and protein, the control of stable RNA and RNA polymerase genes, the functional activities of ribosomes and RNA polymerase, and the control of DNA replication and cell division. With observed values for these parameters, the model system simulates the exponential increase in the number of ribosomes and RNA polymerase molecules, as well as in the amounts of DNA, RNA and protein and in the cell number. The doubling time of this exponential increase and the simulated cell composition (DNA, RNA and protein per cell, or RNA and protein per genome) assume the correct values typical for the culture in which the input parameters were observed, and independent of the zero time conditions of the system which can be arbitrarily chosen. The simulation can be used to check the consistency of observed growth parameters, or to indirectly find the kinetic behavior of growth parameters which cannot be readily observed, or to analyze experiments involving a perturbation of steady-state growth. As examples of the latter, the simulation of a “step-up” experiment is presented in which the effects of a step-wise increase in the DNA replication velocity are analyzed, and the simulation of a nutritional shift-up, in which the kinetic changes in the gene activities for rRNA and rprotein genes are examined.     

The bacterial chromosome

Bacteria represent the vast majority of biological diversity found on Earth. In this review, we focus on selected aspects of their genetic material, those providing insight into structural, functional, dynamic, and evolutionary aspects of their genomes. Bacterial chromosomes are far more dynamic than previously realized, and dozens of mechanisms giving rise to genomic plasticity are now understood. Maturation of the genomics era has provided the tools for unraveling the interwoven details of DNA structure/function relationships that provide a basis for organismal diversity. Some of the most throughly understood processes that underlie the dynamics of genomic structure and function in prokaryotes are examined.     

The bacterial lipocalins

The lipocalins were once regarded as a eukaryotic protein family, but new members have been recently discovered in bacteria. The first bacterial lipocalin (Blc) was identified in Escherichia coli as an outer membrane lipoprotein expressed under conditions of environmental stress. Blc is distinguished from most lipocalins by the absence of intramolecular disulfide bonds, but the presence of a membrane anchor is shared with two of its closest homologues, apolipoprotein D and lazarillo. Several common features of the membrane-anchored lipocalins suggest that each may play an important role in membrane biogenesis and repair. Additionally, Blc proteins are implicated in the dissemination of antibiotic resistance genes and in the activation of immunity. Recent genome sequencing efforts reveal the existence of at least 20 bacterial lipocalins. The lipocalins appear to have originated in Gram-negative bacteria and were probably transferred horizontally to eukaryotes from the endosymbiotic alpha-proteobacterial ancestor of the mitochondrion. The genome sequences also reveal that some bacterial lipocalins exhibit disulfide bonds and alternative modes of subcellular localization, which include targeting to the periplasmic space, the cytoplasmic membrane, and the cytosol. The relationships between bacterial lipocalin structure and function further illuminate the common biochemistry of bacterial and eukaryotic cells.     

Eyeing bacterial genomes

The density of information in a bacterial genome allows its history, organization and encoded functions to be distilled into a single graphical representation. These features have made it possible to discern the forces acting in and on bacterial genomes at levels not attainable in eukaryotes.     

Shuffling bacterial metabolomes

Horizontal gene transfer (HGT) has a far more significant role than gene duplication in bacterial evolution. This has recently been illustrated by work demonstrating the importance of HGT in the emergence of bacterial metabolic networks, with horizontally acquired genes being placed in peripheral pathways at the outer branches of the networks.     

Modelling bacterial speciation

A central problem in understanding bacterial speciation is how clusters of closely related strains emerge and persist in the face of recombination. We use a neutral Fisher-Wright model in which genotypes, defined by the alleles at 140 house-keeping loci, change in each generation by mutation or recombination, and examine conditions in which an initially uniform population gives rise to resolved clusters. Where recombination occurs at equal frequency between all members of the population, we observe a transition between clonal structure and sexual structure as the rate of recombination increases. In the clonal situation, clearly resolved clusters are regularly formed, break up or go extinct. In the sexual situation, the formation of distinct clusters is prevented by the cohesive force of recombination. Where the rate of recombination is a declining log-linear function of the genetic distance between the donor and recipient strain, distinct clusters emerge even with high rates of recombination. These clusters arise in the absence of selection, and have many of the properties of species, with high recombination rates and thus sexual cohesion within clusters and low rates between clusters. Distance-scaled recombination can thus lead to a population splitting into distinct genotypic clusters, a process that mimics sympatric speciation. However, empirical estimates of the relationship between sequence divergence and recombination rate indicate that the decline in recombination is an insufficiently steep function of genetic distance to generate species in nature under neutral drift, and thus that other mechanisms should be invoked to explain speciation in the presence of recombination.     

Dental bacterial plaque

The literature on the subject of dental bacterial plaque is extensive. In spite of considerable research, the mode of its formation together with the variability in bacterial content requires further clarification. Mechanical methods of plaque control are effective but limited in a population sense. Of the numerous chemotherapeutic agents in plaque control, chlorhexidin appears the most effective.