Biology Of Bacteria Research Articles

Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity.

DNA methylations play an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they are important drivers of bacterial evolution interfering in horizontal gene transfer events by providing a defence against foreign DNA invasion or by favouring genetic transfer through production of recombinogenic DNA ends. Little is known regarding the methylome of the Mycoplasma genus, which encompasses several pathogenic species with small genomes. Here, genome-wide detection of DNA methylations was conducted using single molecule real-time (SMRT) and bisulphite sequencing in several strains of Mycoplasma agalactiae , an important ruminant pathogen and a model organism. Combined with whole-genome analysis, this allowed the identification of 19 methylated motifs associated with three orphan methyltransferases (MTases) and eight RM systems. All systems had a homolog in at least one phylogenetically distinct Mycoplasma spp. Our study also revealed that several superimposed genetic events may participate in the M. agalactiae dynamic epigenomic landscape. These included (i) DNA shuffling and frameshift mutations that affect the MTase and restriction endonuclease content of a clonal population and (ii) gene duplication, erosion, and horizontal transfer that modulate MTase and RM repertoires of the species. Some of these systems were experimentally shown to play a major role in mycoplasma conjugative, horizontal DNA transfer. While the versatility of DNA methylation may contribute to regulating essential biological functions at cell and population levels, RM systems may be key in mycoplasma genome evolution and adaptation by controlling horizontal gene transfers.

Oxidative Stress in Bacteria and the Central Dogma of Molecular Biology.

Ever since the “great oxidation event,” Earth’s cellular life forms had to cope with the danger of reactive oxygen species (ROS) affecting the integrity of biomolecules and hampering cellular metabolism circuits. Consequently, increasing ROS levels in the biosphere represented growing stress levels and thus shaped the evolution of species. Whether the ROS were produced endogenously or exogenously, different systems evolved to remove the ROS and repair the damage they inflicted. If ROS outweigh the cell’s capacity to remove the threat, we speak of oxidative stress. The injuries through oxidative stress in cells are diverse. This article reviews the damage oxidative stress imposes on the different steps of the central dogma of molecular biology in bacteria, focusing in particular on the RNA machines involved in transcription and translation.

Bacterial extracellular vesicles: Understanding biology promotes applications as nanopharmaceuticals

Extracellular vesicle (EV)-mediated communication between proximal and distant cells is a highly conserved characteristic in all of the life domains, including bacteria. These vesicles that contain a variety of biomolecules, such as proteins, lipids, nucleic acids, and small-molecule metabolites play a key role in the biology of bacteria. They are one of the key underlying mechanisms behind harmful or beneficial effects of many pathogenic, symbiont, and probiotic bacteria. These nanoscale EVs mediate extensive crosstalk with mammalian cells and deliver their cargos to the host. They are stable in physiological condition, can encapsulate diverse biomolecules and nanoparticles, and their surface could be engineered with available technologies. Based on favorable characteristics of bacterial vesicles, they can be harnessed for designing a diverse range of therapeutics and diagnostics for treatment of disorders including tumors and resistant infections. However, technical limitations for their production, purification, and characterization must be addressed in future studies.

Integrative in-cell structural biology

Structural Biology In bacteria, RNA polymerases can associate with ribosomes to form transcription-translation units called expressomes. Multiple models based on structural data of in vitro reconstitution assays have been proposed for how the two machineries interface with one another. Understanding this bacteria-specific coupling mechanism offers insight regarding the central dogma of molecular biology and might be leveraged for antibiotic development. O'Reilly et al. found that the NusA protein interfaces between the two complexes. The authors combined cryo–electron tomography and cross-linking mass spectrometry to produce an integrative model of the transcribing, translating expressome of Mycoplasma pneumoniae obtained entirely from in-cell data. This approach contributes to the development of in-cell structural biology. Science , this issue p. [554][1] [1]: /lookup/doi/10.1126/science.abb3758

Indirect Bacterial Transcription-Translation Coupling Mechanism Revealed by In Situ Integrative Structural Biology

In situ structural biology aims to resolve macromolecular structures and collective behaviors of macromolecular machineries within the cell. In bacteria, transcription mediated by RNA polymerase is known to be functionally coupled to the leading ribosome, a process crucial for efficient gene expression. Direct ribosome-RNA polymerase interaction has been demonstrated in vitro, but how these two gigantic molecular machines coordinate is yet unclear, especially within the context of crowded and complex cellular environments. Using Mycoplasma pneumonia as model system, we integrated cellular cryo-electron tomography followed by sub-tomogram analysis (STA) and in-cell crosslinking mass spectrometry (CLMS) to investigate the coupling in native cells, without resorting to labelling or cell disruption. By averaging sub-tomograms extracted in silico from cellular volumes, we solved the 70S ribosome structure at 6.4 Å resolution, so far the highest resolution reported for in-cell cryo-ET. After large-scale classification, we determined the structure of a super-complex consisting of ribosome, RNA polymerase and other auxiliary proteins. Protein-protein interaction networks revealed by in-cell CLMS indicated an essential transcription elongation factor bridging RNA polymerase and the translating ribosome. Integrative modelling suggests a novel, indirect transcription-translation coupling mechanism, which advances our understanding of key machineries of the central dogma of molecular biology in bacteria. Methodology wise, our work demonstrates the feasibility and superiority of integrative structural biology performed directly inside cells. Integration of two approaches, cryo-ET/STA and in-cell CLMS, holds great potential to delineate cellular processes in a quantitative and structural view.

Iac Gene Expression in the Indole-3-Acetic Acid-Degrading Soil Bacterium Enterobacter soli LF7.

We show for soil bacterium Enterobacter soli LF7 that the possession of an indole-3-acetic acid catabolic (iac) gene cluster is causatively linked to the ability to utilize the plant hormone indole-3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes, chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (<1%) differentially expressed genes in response to IAA. Also highly induced and immediately downstream of the iac cluster were genes for a major facilitator superfamily protein (mfs) and enzymes of the β-ketoadipate pathway (pcaIJD-catBCA), which channels catechol into central metabolism. This entire iacHABICDEFG-mfs-pcaIJD-catBCA gene set was constitutively expressed in an iacR deletion mutant, confirming the role of iacR, annotated as coding for a MarR-type regulator and located upstream of iacH, as a repressor of iac gene expression. In E. soli LF7 carrying the DNA region upstream of iacH fused to a promoterless gfp gene, green fluorescence accumulated in response to IAA at concentrations as low as 1.6 μM. The iacH promoter region also responded to chlorinated IAA, but not other aromatics tested, indicating a narrow substrate specificity. In an iacR deletion mutant, gfp expression from the iacH promoter region was constitutive, consistent with the predicted role of iacR as a repressor. A deletion analysis revealed putative -35/-10 promoter sequences upstream of iacH, as well as a possible binding site for the IacR repressor.IMPORTANCE Bacterial iac genes code for the enzymatic conversion of the plant hormone indole-3-acetic acid (IAA) to catechol. Here, we demonstrate that the iac genes of soil bacterium Enterobacter soli LF7 enable growth on IAA by coarrangement and coexpression with a set of pca and cat genes that code for complete conversion of catechol to central metabolites. This work contributes in a number of novel and significant ways to our understanding of iac gene biology in bacteria from (non-)plant environments. More specifically, we show that LF7's response to IAA involves derepression of the MarR-type transcriptional regulator IacR, which is quite fast (less than 25 min upon IAA exposure), highly specific (only in response to IAA and chlorinated IAA, and with few genes other than iac, cat, and pca induced), relatively sensitive (low micromolar range), and seemingly tailored to exploit IAA as a source of carbon and energy.

Bacterial colonies as complex adaptive systems

The present work explores bacterial colonies and their individual and social behaviours under the lens of complex adaptive systems. We initially provide a background on the biology of bacteria to describe important phenomena, such as quorum-sensing, individual and collective behaviours, adaptation, evolution and self-organization over the influence of mechanical effects on bacterial systems and connecting scales. We then explore some associations between bacterial colonies and complex adaptive systems by considering components and ownerships of self-organization. The main contribution of this paper places emphasis on individual decision-making and behaviour as a cause of bacterial colonies’ actions, i.e., how self-organization and collective behaviours impact the ability of a bacterial colony to address an environmental stimulus and maintain itself as an open biological and fault-tolerant system. Finally, we conclude the work and provide some comments regarding future research.

Human pleural fluid is a potent growth medium for Streptococcus pneumoniae.

Empyema is defined by the presence of bacteria and/or pus in pleural effusions. However, the biology of bacteria within human pleural fluid has not been studied. Streptococcus pneumoniae is the most common cause of pediatric and frequent cause of adult empyema. We investigated whether S. pneumoniae can proliferate within human pleural fluid and if growth is affected by the cellular content of the fluid and/or characteristics of pneumococcal surface proteins. Invasive S. pneumoniae isolates (n = 24) and reference strain recovered from human blood or empyema were inoculated (1.5×106CFU/mL) into sterile human malignant pleural fluid samples (n = 11). All S. pneumoniae (n = 25) strains proliferated rapidly, increasing by a median of 3009 (IQR 1063–9846) from baseline at 24hrs in all pleural effusions tested. Proliferation was greater than in commercial pneumococcal culture media and concentrations were maintained for 48hrs without autolysis. A similar magnitude of proliferation was observed in pleural fluid before and after removal of its cellular content, p = 0.728. S. pneumoniae (D39 strain) wild-type, and derivatives (n = 12), each with mutation(s) in a different gene required for full virulence were inoculated into human pleural fluid (n = 8). S. pneumoniae with pneumococcal surface antigen A (ΔpsaA) mutation failed to grow (2207-fold lower than wild-type), p<0.001, however growth was restored with manganese supplementation. Growth of other common respiratory pathogens (n = 14) across pleural fluid samples (n = 7) was variable and inconsistent, with some strains failing to grow. We establish for the first time that pleural fluid is a potent growth medium for S. pneumoniae and proliferation is dependent on the PsaA surface protein and manganese.

CRISPR/Cas9: Transcending the Reality of Genome Editing.

With the expansion of the microbiology field of research, a new genome editing tool arises from the biology of bacteria that holds the promise of achieving precise modifications in the genome with a simplicity and versatility that surpasses previous genome editing methods. This new technique, commonly named CRISPR/Cas9, led to a rapid expansion of the biomedical field; more specifically, cancer characterization and modeling have benefitted greatly from the genome editing capabilities of CRISPR/Cas9. In this paper, we briefly summarize recent improvements in CRISPR/Cas9 design meant to overcome the limitations that have arisen from the nuclease activity of Cas9 and the influence of this technology in cancer research. In addition, we present challenges that might impede the clinical applicability of CRISPR/Cas9 for cancer therapy and highlight future directions for designing CRISPR/Cas9 delivery systems that might prove useful for cancer therapeutics.

The Importance of Role Models in Research.

The Importance of Role Models in Research.

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.

Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.

Editorial: RNA in bacteria: biogenesis, regulatory mechanisms and functions

The advent of high-throughput computational and RNA sequencing approaches in the past decade has highlighted an increasing number of RNA molecules in bacteria with critical functions in metabolic, physiological and virulence processes. Accordingly, proteins that interact with RNA have also benefited from a regained interest. A multitude of mechanisms involved in the regulation of gene expression by RNA molecules and in the interaction of RNAs with molecular partners have been described. There is a growing curiosity in understanding how RNA interferes or interacts with target DNA, RNA and proteins, and in the identification and characterization of nucleases, RNA helicases or RNA chaperones responsible for the activation, stability, decay or modes of action of RNA molecules. Remarkably, the recent analysis of CRISPR-Cas systems as RNA-mediated adaptive immune pathways in bacteria and archaea has resulted in the identification of novel families of proteins that function alone or in complexes to interact with RNA and/or DNA, and novel mechanisms of nucleic acid-based interference herewith. Information is now available on a large and still growing number of bacterial RNA molecules, the targets and functions of which are largely unknown. Given the enormous heterogeneity among different bacteria and the constant pressure for adaptation to multiple stresses and environments, we expect to discover a wide variety of novel RNAs with regulatory functions and associated proteins. We predict exciting findings and innovation in the field of RNA research in bacteria for a number of years to come. In this issue, FEMS Microbiology Reviews has selected a series of articles that highlight some of the recent findings on RNA biology in bacteria focusing on RNA biogenesis, modes of action, regulatory mechanisms and functions. The continuous effort to adapt innovative technologies and biological approaches to the bacterial RNA field has advanced our understanding of how regulatory RNAs and their … [↵][1]* Corresponding editors. E-mail: emmanuelle.charpentier{at}helmholtz-hzi.de and wolfgang.hess{at}biologie.uni-freiburg.de [1]: #xref-corresp-1-1

Les animaux vertébrés et les maladies dues à des bactéries vectorisées par les tiques

SUMMARY Vertebrate animals and diseases induced by tickborne bacteria Vertebrate animals (mammals, birds, and reptiles) occupy a prominent place in the biology of bacteria transmitted by ticks, as reservoirs of bacteria but also allowing the reproductive cycle of vector ticks. In addition, domesticated animals express clinical presentations similar to those described in humans and laboratory diagnosis use globally the same techniques. This paper presents the main diseases caused by tick-borne bacteria: Lyme disease caused by Borrelia burgdorferi, a bacteria with varied animal reservoirs (small wild mammals, birds, lizards) and which infects several domestic animal species; granulocytic anaplasmosis due to Anaplasma phagocytophilum whose economic consequences for cattle are important; bartonellosis due to Bartonella vinsonii berkhoffii and rikettsiosis due to Rickettsia conorii (Mediterranean spotted fever) and R. slovaca (tick borne lymphadenopathy/ TIBOLA). Epidemiological and clinical aspects, and diagnosis are discussed for each of the diseases. Tick – Anaplasma phagocytophilum – Borrelia burgdorferi – Bartonella vinsonii berkhoffii – Rickettsia conorii – R. slovaca

The Brucella abortus General Stress Response System Regulates Chronic Mammalian Infection and Is Controlled by Phosphorylation and Proteolysis

Virulence of pathogenic bacteria is often determined by their ability to adapt to stress. The Brucella abortus general stress response (GSR) system is required for chronic mammalian infection and is regulated by phosphorylation and proteolysis. The B. abortus GSR signaling pathway has multiple layers of post-translational control and is a determinant of chronic infection. This study provides new, molecular level insight into chronic Brucella infection. Brucella spp. are adept at establishing a chronic infection in mammals. We demonstrate that core components of the α-proteobacterial general stress response (GSR) system, PhyR and σ(E1), are required for Brucella abortus stress survival in vitro and maintenance of chronic murine infection in vivo. ΔphyR and ΔrpoE1 null mutants exhibit decreased survival under acute oxidative and acid stress but are not defective in infection of primary murine macrophages or in initial colonization of BALB/c mouse spleens. However, ΔphyR and ΔrpoE1 mutants are attenuated in spleens beginning 1 month postinfection. Thus, the B. abortus GSR system is dispensable for colonization but is required to maintain chronic infection. A genome-scale analysis of the B. abortus GSR regulon identified stress response genes previously linked to virulence and genes that affect immunomodulatory components of the cell envelope. These data support a model in which the GSR system affects both stress survival and the interface between B. abortus and the host immune system. We further demonstrate that PhyR proteolysis is a unique feature of GSR control in B. abortus. Proteolysis of PhyR provides a mechanism to avoid spurious PhyR protein interactions that inappropriately activate GSR-dependent transcription. We conclude that the B. abortus GSR system regulates acute stress adaptation and long term survival within a mammalian host and that PhyR proteolysis is a novel regulatory feature in B. abortus that ensures proper control of GSR transcription.

Editorial [Hot Topic: Evolutionary Systems Biology (Guest Editor: Jianying Gu)

Systems biology has a long history as a theoretical framework in biology, positing that cellular systems possess emergent properties that can only be explained by the interactions among the components of an organism rather than by any individual component in itself. With the advent of the genomic era, data sets encompassing systems-wide measurements of gene complements, transcription, and protein expression are becoming available. Thoughtful integration of these data can lead to a systems-level understanding of the components and dynamics of cellular machineries and the development of practical methods for inferring and constructing network models of these interactions is well under way. As the creation of plausible network models of cellular systems becomes possible, comparison of systems in an evolutionary light promises to reveal the evolutionary forces that shape these systems. Systems are dynamic and selectable, that is, they respond to pressures brought to bear by changes in their environment. Therefore, the application of the methods of evolutionary biology within a systems biology framework can aid in identifying the concerted changes that drive the emergence of new phenotypes. A better understanding of systems evolution will greatly advance our knowledge about the complexity of gene regulation and help identify new therapeutic targets for effective treatment of various diseases. This special issue of Current Genomics is intended to provide a forum for researchers to share their experiences on all aspects of genome and systems evolution. This issue includes a review article discussing about the proteomics techniques that are capable of generating high quality data for systems biology research: Chen et al. reviewed recent advances in proteolysis, a key procedure prior to mass spectrometry and peptide mapping in proteomic studies of gene function. They showed that the proteolysis strategies can be accelerated by various electromagnetic waves, such as microwave-accelerated protein digestion, infrared-assisted proteolysis, ultraviolet-enhanced protein digestion, laser-assisted proteolysis, and future prospects. This issue also includes two review articles with a special emphasis on the systems biology of bacteria, ideal model organisms for evolutionary analyses of genome plasticity and adaptive phenotypes. Tang's review is focused on microbial metabolomics, which involves fast, high throughput characterization of the metabolite complements of a microorganism, and thus summarizes the global outcome of the interplay between the developmental processes and the environment. Selected topics illustrate the impact of metabolomics on the understanding of systems microbiology. Zhou et al. provide an overview of the recent advances in Streptomyces biology that have been driven by high throughput technologies. The omics based studies have revolutionized the understanding of system control and regulation dynamics of this group of bacterial of medicinal and industrial importance. Evolutionary systems biology approaches have also been applied to biomedical studies. Cai et al. provide a phylogenomic overview of the origin, distribution, diversity, and evolution of malarial proteases, a class of promising therapeutic targets for combating this devastating infectious disease that is responsible for over 1 million deaths yearly. Klemcke et al. introduce a novel physiogenomic approach to the study of hemorraghic shock, a major cause of death throughout the world. Their findings in heritable quantitative trait loci, as well as potential epigenetic mechanisms that might influence survival time after severe hemorrhage, may lead to the improvement in survival of traumatic hemorrhage and provide knowledge of genetically-informed personalized treatments. Overall, these reviews provide a fascinating survey of the combination of systems thinking and evolutionary analysis across the biological spectrum. As modeling approaches improve and as more data from more species become available, the study of systems evolution will clarify the links among the genotype, the phenotype and the selective pressures arising from the organism’s place in the environment. As an emerging field in the post genomic era, evolutionary systems biology promises to make profound contributions to our understanding of life.

All together now: Integrating biofilm research across disciplines.

Bacterial biofilms are integrated, multi-species communities of cells that adhere to almost any surface and are fundamental to the ecology and biology of bacteria. Not only do biofilms contribute to human health and disease, they also play important roles in the context of energy and the environment. The formation of biofilms requires interactions between bacteria and the surfaces they colonize, and both microbe and surface can impact the structure, function, and composition of these communities. Bacteria in biofilms exhibit surprisingly sophisticated social behavior, both cooperative and competitive, made possible by their cell biology. However, they are also hierarchically organized systems governed by complex physical and chemical interactions. Because of this, the study of bacterial biofilms has recently attracted the attention of materials scientists, physicists, chemists, and nanotechnology experts who import not only new tools, but also new concepts and perspectives. This issue reviews recent progress in multidisciplinary studies of biofilms.

Harnessing the Power of Microbial Genomics for Exploring Exceptions and Shifting Perceptions

Harnessing the Power of Microbial Genomics for Exploring Exceptions and Shifting Perceptions

Small Cells—Big Future

Small Cells—Big Future

ABC Transporters Involved in Export of Cell Surface Glycoconjugates

Complex glycoconjugates play critical roles in the biology of microorganisms. Despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. One of the primary pathways involves representatives of the ATP-binding cassette (ABC) transporter superfamily. These proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both Gram-positive and Gram-negative bacteria. Recent investigations of the structure and function of ABC transporters involved in the export of lipopolysaccharide O antigens have revealed two fundamentally different strategies for coupling glycan polymerization to export. These mechanisms are distinguished by the presence (or absence) of characteristic nonreducing terminal modifications on the export substrates, which serve as chain termination and/or export signals, and by the presence (or absence) of a discrete substrate-binding domain in the nucleotide-binding domain polypeptide of the ABC transporter. A bioinformatic survey examining ABC exporters from known oligo- and polysaccharide biosynthesis loci identifies conserved nucleotide-binding domain protein families that correlate well with themes in the structures and assembly of glycans. The familial relationships among the ABC exporters generate hypotheses concerning the biosynthesis of structurally diverse oligo- and polysaccharides, which play important roles in the biology of bacteria with different lifestyles.

Bacterial extracellular biology

Why extracellular biology? For the first few decades after the discovery of bacterial genetics, fundamental studies of the molecular and cellular biology of bacteria focused on the biochemical pathways and biosynthetic mechanisms of the growth and division of single-celled organisms, particularly Escherichia coli K-12. This revealed mostly the features universal among bacteria – and these are generally either cytoplasmic or intimately associated with the cell. Gradually, genetic techniques were also applied to a greater diversity of bacteria in order to understand aspects of their biology that were not universal, but were specific to particular groups. By the late 1980s, it was emerging that extracellular biology played a significant part in, for example, bacterial luminescence, antibiotic biosynthesis, multicellular development, virulence, pathogenicity and symbiosis – all processes whose end results also had extracellular implications. In the 20 years since then, the genomic revolution …