Thioesterase YbgC affects motility by modulating c-di-GMP levels in Shewanella oneidensis

The Tol-Pal System Plays an Important Role in Maintaining Cell Integrity During Elongation in Escherichia coli

The Tol-Pal system is a transenvelope complex widely conserved among Gram-negative bacteria. It is recruited to the septal ring during cytokinesis, and its inactivation causes pleiotropic phenotypes mainly associated with the division process. From our genetic screen to identify factors required for delaying lysis upon treatment of beta lactams, we discovered that the tol-pal mutant shares similar defects with mutants of the major class A PBP system (PBP1b-LpoB) in terms of lysis prevention. Further phenotypic analyses revealed that the Tol-Pal system plays an important role in maintaining cell integrity not only during septation, but also during cell elongation. Simultaneous inactivation of the Tol-Pal system and the PBP1b-LpoB system leads to lysis during cell elongation as well as during division. Moreover, production of the Lpo activator-bypass PBP1b, but not wild-type PBP1b, partially suppressed the Tol-Pal defect in maintaining cell integrity upon treatment of mecillinam specific for the Rod system, suggesting that the Tol-Pal system is likely to be involved in the activation of aPBP by Lpo factors. Overall, our results indicate that the Tol-Pal system plays an important role in maintaining cell wall integrity during elongation in addition to its multifaceted roles during cytokinesis.

Thioesterase enzyme families: Functions, structures, and mechanisms

Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity. Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.

Functional roles of multiple Ton complex genes in a Sphingobium degrader of lignin-derived aromatic compounds

TonB-dependent transporters (TBDTs) mediate outer membrane transport of nutrients using the energy derived from proton motive force transmitted from the TonB–ExbB–ExbD complex localized in the inner membrane. Recently, we discovered ddvT encoding a TBDT responsible for the uptake of a 5,5-type lignin-derived dimer in Sphingobium sp. strain SYK-6. Furthermore, overexpression of ddvT in an SYK-6-derivative strain enhanced its uptake capacity, improving the rate of platform chemical production. Thus, understanding the uptake system of lignin-derived aromatics is fundamental for microbial conversion-based lignin valorization. Here we examined whether multiple tonB-, exbB-, and exbD-like genes in SYK-6 contribute to the outer membrane transport of lignin-derived aromatics. The disruption of tonB2–6 and exbB3 did not reduce the capacity of SYK-6 to convert or grow on lignin-derived aromatics. In contrast, the introduction of the tonB1–exbB1–exbD1–exbD2 operon genes into SYK-6, which could not be disrupted, promoted the conversion of β-O-4-, β-5-, β-1-, β-β-, and 5,5-type dimers and monomers, such as ferulate, vanillate, syringate, and protocatechuate. These results suggest that TonB-dependent uptake involving the tonB1 operon genes is responsible for the outer membrane transport of the above aromatics. Additionally, exbB2/tolQ and exbD3/tolR were suggested to constitute the Tol-Pal system that maintains the outer membrane integrity.

Recruitment of the TolA protein to cell constriction sites in Escherichia coli via three separate mechanisms, and a critical role for FtsWI activity in recruitment of both TolA and TolQ

The Tol-Pal system of Gram-negative bacteria helps maintain integrity of the cell envelope and ensures that invagination of the envelope layers during cell fission occurs in a well-coordinated manner. In E. coli, the five Tol-Pal proteins (TolQ, R, A, B and Pal) accumulate at cell constriction sites in a manner that normally requires the activity of the cell constriction initiation protein FtsN. While septal recruitment of TolR, TolB and Pal also requires the presence of TolQ and/or TolA, each of the the latter two can recognize constriction sites independently of the other system proteins. What attracts TolQ or TolA to these sites is unclear. We show that FtsN attracts both proteins in an indirect fashion, and that PBP1A, PBP1B and CpoB are dispensable for their septal recruitment. However, the β-lactam aztreonam readily interferes with septal accumulation of both TolQ and TolA, indicating that FtsN-stimulated production of septal peptidoglycan by the FtsWI synthase is critical to their recruitment. We also discovered that each of TolA's three domains can recognize division sites in a separate fashion. Notably, the middle domain (TolAII) is responsible for directing TolA to constriction sites in the absence of other Tol-Pal proteins and CpoB, while recruitment of TolAI and TolAIII requires TolQ and a combination of TolB, Pal, and CpoB, respectively. Additionally, we describe the construction and use of functional fluorescent sandwich fusions of the ZipA division protein, which should be more broadly valuable in future studies of the E. coli cell division machinery. IMPORTANCE Cell division (cytokinesis) is a fundamental biological process that is incompletely understood for any organism. Division of bacterial cells relies on a ring-like machinery called the septal ring or divisome that assembles along the circumference of the mother cell at the site where constriction will eventually occur. In the well-studied bacterium Escherichia coli, this machinery contains over thirty distinct proteins. We studied how two such proteins, TolA and TolQ, which also play a role in maintaining integrity of the outer-membrane, are recruited to the machinery. We find that TolA can be recruited by three separate mechanisms, and that both proteins rely on the activity of a well-studied cell division enzyme for their recruitment.

Promoting Extracellular Electron Transfer of Shewanella oneidensis MR-1 by Optimizing the Periplasmic Cytochrome c Network

The low efficiency of extracellular electron transfer (EET) is a major bottleneck for Shewanella oneidensis MR-1 acting as an electroactive biocatalyst in bioelectrochemical systems. Although it is well established that a periplasmic c-type cytochrome (c-Cyt) network plays a critical role in regulating EET efficiency, the understanding of the network in terms of structure and electron transfer activity is obscure and partial. In this work, we attempted to systematically investigate the impacts of the network components on EET in their absence and overproduction individually in microbial fuel cell (MFC). We found that overexpression of c-Cyt CctA leads to accelerated electron transfer between CymA and the Mtr system, which function as the primary quinol oxidase and the outer-membrane (OM) electron hub in EET. In contrast, NapB, FccA, and TsdB in excess severely impaired EET, reducing EET capacity in MFC by more than 50%. Based on the results from both strategies, a series of engineered strains lacking FccA, NapB, and TsdB in combination while overproducing CctA were tested for a maximally optimized c-Cyt network. A strain depleted of all NapB, FccA, and TsdB with CctA overproduction achieved the highest maximum power density in MFCs (436.5 mW/m²), ∼3.62-fold higher than that of wild type (WT). By revealing that optimization of periplasmic c-Cyt composition is a practical strategy for improving EET efficiency, our work underscores the importance in understanding physiological and electrochemical characteristics of c-Cyts involved in EET.

L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation

L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.

The multifarious roles of Tol-Pal in Gram-negative bacteria

In the 1960s several groups reported the isolation and preliminary genetic mapping of Escherichia coli strains tolerant towards the action of colicins. These pioneering studies kick-started two new fields in bacteriology; one centred on how bacteriocins like colicins exploit the Tol (or more commonly Tol-Pal) system to kill bacteria, the other on the physiological role of this cell envelope-spanning assembly. The following half century has seen significant advances in the first of these fields whereas the second has remained elusive, until recently. Here, we review work that begins to shed light on Tol-Pal function in Gram-negative bacteria. What emerges from these studies is that Tol-Pal is an energised system with fundamental, interlinked roles in cell division – coordinating the re-structuring of peptidoglycan at division sites and stabilising the connection between the outer membrane and underlying cell wall. This latter role is achieved by Tol-Pal exploiting the proton motive force to catalyse the accumulation of the outer membrane peptidoglycan associated lipoprotein Pal at division sites while simultaneously mobilising Pal molecules from around the cell. These studies begin to explain the diverse phenotypic outcomes of tol-pal mutations, point to other cell envelope roles Tol-Pal may have and raise many new questions.

Characterization of Burkholderia cepacia Complex Core Genome and the Underlying Recombination and Positive Selection

Recombination and positive selection are two key factors that play a vital role in pathogenic microorganisms’ population adaptation and diversification. The Burkholderia cepacia complex (Bcc) represents bacterial species with high similarity, which can cause severe infections among cases suffering from the chronic granulomatous disorder and cystic fibrosis (CF). At present, no genome-wide study has been carried out focusing on investigating the core genome of Bcc associated with the two evolutionary forces. The general characteristics of the core genome of Bcc species remain scarce as well. In this study, we explored the core orthologous genes of 116 Bcc strains using comparative genomic analysis and studied the two adaptive evolutionary forces: recombination and positive selection. We estimated 1005 orthogroups consisting entirely of single copy genes. These single copy orthologous genes in some Cluster of Orthologous Groups (COG) categories showed significant differences in the comparison of several evolutionary properties, and the encoding proteins were relatively simple and compact. Our findings showed that 5.8% of the core orthologous genes strongly supported recombination; in the meantime, 1.1% supported positive selection. We found that genes involved in protein synthesis as well as material transport and metabolism are favored by selection pressure. More importantly, homologous recombination contributed more genetic variation to a large number of genes and largely maintained the genetic cohesion in Bcc. This high level of recombination between Bcc species blurs their taxonomic boundaries, which leads Bcc species to be difficult or impossible to distinguish phenotypically and genotypically.

Structure, function, and regulation of thioesterases

Thioesterases are present in all living cells and perform a wide range of important biological functions by catalysing the cleavage of thioester bonds present in a diverse array of cellular substrates. Thioesterases are organised into 25 families based on their sequence conservation, tertiary and quaternary structure, active site configuration, and substrate specificity. Recent structural and functional characterisation of thioesterases has led to significant changes in our understanding of the regulatory mechanisms that govern enzyme activity and their respective cellular roles. The resulting dogma changes in thioesterase regulation include mechanistic insights into ATP and GDP-mediated regulation by oligomerisation, the role of new key regulatory regions, and new insights into a conserved quaternary structure within TE4 family members. Here we provide a current and comparative snapshot of our understanding of thioesterase structure, function, and regulation across the different thioesterase families.

Flagellation of Shewanella oneidensis Impacts Bacterial Fitness in Different Environments

Flagella occur on many prokaryotes, which primarily propel cells to move from detrimental to favorable environments. A variety of species-specific flagellation patterns have been identified. Although it is presumed that for each of these flagellated microorganisms, an evolutionarily fixed flagellation pattern is favored under the normal living conditions, direct evidence is lacking. Here, we use Shewanella oneidensis, a rod-shaped Gram-negative bacterium with a monotrichous polar flagellum (MR-1, the wild-type), as a research model. The investigation has been enabled by multiple mutants with diverse flagellation patterns that had been generated by removing FlhF and FlhG proteins that control flagellar location and number, respectively. Growth assays, as a measure of fitness, revealed that the wild-type strain predominated in spreading on swim plates and in pellicles which form at the air-liquid interface. However, under the pellicles where oxygen is limited, both aflagellated and monotrichous lateral strains showed similar increase in fitness, whereas strains with multiple flagella were less competitive. Moreover, under shaking culturing conditions, the aflagellated strain outcompeted all other strains, including the wild-type, suggesting that cells devoid of flagella would be more likely enriched upon agitation. Overall, these data support the presumption that the monotrichous polar flagellum, as evolutionarily fixed in the wild-type strain, is optimal for the growth fitness of S. oneidensis over any other mutants under most test conditions. However, upon specific changes of environmental conditions, another form could come to predominate. These findings provide insight into the impacts of flagellation patterns and function on bacterial adaptation to differing environments.

Screening for Diguanylate Cyclase (DGC) Inhibitors Mitigating Bacterial Biofilm Formation

The majority of bacteria in the natural environment organize themselves into communal biofilms. Biofilm formation benefits bacteria conferring resistance to harmful molecules (e.g., antibiotics, disinfectants, and host immune factors) and coordinating their gene expression through quorum sensing (QS). A primary signaling molecule promoting bacterial biofilm formation is the universal second messenger cyclic di-GMP. This dinucleotide predominantly controls the gene expression of motility, adhesins, and capsule production to coordinate biofilm formation. Cyclic di-GMP is synthesized by diguanylate cyclases (DGCs) that have a GGDEF domain and is degraded by phosphodiesterases (PDEs) containing either an EAL or an HD-GYP domain. Since high cellular c-di-GMP concentrations are correlated with promoting the ability of bacteria to form biofilms, numerous research endeavors to identify chemicals capable of inhibiting the c-di-GMP synthesis activity of DGCs have been performed in order to inhibit bacterial biofilm formation. This review describes currently identified chemical inhibitors that disturb the activity of DGCs and the methods of screening and assay for their discovery.

Oxidized OxyR Up-Regulates ahpCF Expression to Suppress Plating Defects of oxyR- and Catalase-Deficient Strains

It is well established that in bacteria, such as Escherichia coli, OxyR is a transcriptional regulator that mediates the response to H₂O₂ by activating the OxyR regulon, which consists of many genes that play vital roles in oxidative stress resistance. In Shewanella, OxyR regulates, however, in both reduced and oxidized states, the production of H₂O₂ scavengers, including major catalase KatB and NADH peroxidase AhpCF. Here we showed that the oxyR mutant carried a plating defect manifested as division arresting, a phenotype that can be completely suppressed by an OxyR variant constitutively existing in oxidized form (OxyR^L197P). This effect of OxyR^L197P could not be solely attributed to the increment in KatB production, since the suppression was also observed in the absence of KatB. Although expression of peroxidase CcpA was greatly activated by OxyR^L197P, the contribution of the protein in alleviating plating defect was negligible. We eventually identified AhpCF as the critical factor, when produced at substantially elevated levels by OxyR^L197P, to protect the cell from H₂O₂ attack. Our data indicate that AhpCF is a particularly important peroxidase in oxidative stress resistance in Shewanella, not only playing a compensatory role for catalase, but also by itself providing sufficient protection from killing of H₂O₂ generated abiotically.