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Microorganisms Apr 2021A fundamental question in biology is how cell shapes are genetically encoded and enzymatically generated. Prevalent shapes among walled bacteria include spheres and... (Review)
Review
A fundamental question in biology is how cell shapes are genetically encoded and enzymatically generated. Prevalent shapes among walled bacteria include spheres and rods. These shapes are chiefly determined by the peptidoglycan (PG) cell wall. Bacterial division results in two daughter cells, whose shapes are predetermined by the mother. This makes it difficult to explore the origin of cell shapes in healthy bacteria. In this review, we argue that the Gram-negative bacterium is an ideal model for understanding PG assembly and bacterial morphogenesis, because it forms rods and spheres at different life stages. Rod-shaped vegetative cells of can thoroughly degrade their PG and form spherical spores. As these spores germinate, cells rebuild their PG and reestablish rod shape without preexisting templates. Such a unique sphere-to-rod transition provides a rare opportunity to visualize de novo PG assembly and rod-like morphogenesis in a well-established model organism.
PubMed: 33923279
DOI: 10.3390/microorganisms9050916 -
MSphere May 2021Hsp70 proteins are among the most ubiquitous chaperones and play important roles in maintaining proteostasis and resisting environmental stress. Multiple copies of...
Hsp70 proteins are among the most ubiquitous chaperones and play important roles in maintaining proteostasis and resisting environmental stress. Multiple copies of Hsp70s are widely present in eukaryotic cells with redundant and divergent functions, but they have been less well investigated in prokaryotes. DK1622 is annotated as having many genes. In this study, we performed a bioinformatic analysis of Hsp70 proteins and investigated the functions of six genes in DK1622, including two genes that encode proteins with the conserved PRK00290 domain (MXAN_3192 and MXAN_6671) and four genes that encode proteins with the cl35085 or cd10170 domain. We found that only MXAN_3192 is essential for cell survival and heat shock induction. MXAN_3192, compared with the other genes, has a high transcriptional level, far exceeding that of any other gene, which, however, is not the reason for its essentiality. Deletion of MXAN_6671 () led to multiple deficiencies in development, social motility, and oxidative resistance, while deletion of each of the other four genes decreased sporulation and oxidative resistance. MXAN_3192 or , but not the other genes, restored the growth deficiency of the mutant. Our results demonstrated that the PRK00290 proteins play a central role in the complex cellular functions of , while the other diverse Hsp70 superfamily homologues probably evolved as helpers with some unknown specific functions. Hsp70 proteins are highly conserved chaperones that occur in all kingdoms of life. Multiple copies of Hsp70s are often present in genome-sequenced prokaryotes, especially taxa with complex life cycles, such as myxobacteria. We investigated the functions of six genes in DK1622 and demonstrated that the two Hsp70 proteins with the PRK00290 domain play a central role in complex cellular functions in , while other Hsp70 proteins probably evolved as helpers with some unknown specific functions.
Topics: Bacterial Proteins; Computational Biology; HSP72 Heat-Shock Proteins; Myxococcus xanthus; Phylogeny; Stress, Physiological; Transcription, Genetic
PubMed: 34011688
DOI: 10.1128/mSphere.00305-21 -
Microorganisms Nov 2020As prokaryotes diverge by evolution, essential 'core' genes required for conserved phenotypes are preferentially retained, while inessential 'accessory' genes are lost...
As prokaryotes diverge by evolution, essential 'core' genes required for conserved phenotypes are preferentially retained, while inessential 'accessory' genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera ( and ), and on a species within each genus ( and ). Four new genome sequences are also described here. Despite accessory genes accounting for substantial proportions of each myxobacterial genome, signalling proteins were found to be enriched in the core genome, with two-component system genes almost exclusively so. We also investigated the conservation of signalling proteins in three myxobacterial behaviours. The linear carotenogenesis pathway was entirely conserved, with no gene gain/loss observed. However, the modular fruiting body formation network was found to be evolutionarily plastic, with dispensable components in all modules (including components required for fruiting in the model myxobacterium DK1622). Quorum signalling (QS) is thought to be absent from most myxobacteria, however, they generally appear to be able to produce CAI-I (cholerae autoinducer-1), to sense other QS molecules, and to disrupt the QS of other organisms, potentially important abilities during predation of other prokaryotes.
PubMed: 33171896
DOI: 10.3390/microorganisms8111739 -
MSystems Oct 2023Understanding the processes behind bacterial biofilm formation, maintenance, and dispersal is essential for addressing their effects on health and ecology. Within these...
Understanding the processes behind bacterial biofilm formation, maintenance, and dispersal is essential for addressing their effects on health and ecology. Within these multicellular communities, various cues can trigger differentiation into distinct cell types, allowing cells to adapt to their specific local environment. The soil bacterium forms biofilms in response to starvation, marked by cells aggregating into mounds. Some aggregates persist as spore-filled fruiting bodies, while others disperse after initial formation for unknown reasons. Here, we use a combination of cell tracking analysis and computational simulations to identify behaviors at the cellular level that contribute to aggregate dispersal. Our results suggest that cells in aggregates actively determine whether to disperse or persist and undergo a transition to sporulation based on a self-produced cue related to the aggregate size. Identifying these cues is an important step in understanding and potentially manipulating bacterial cell-fate decisions.
Topics: Spores, Bacterial; Myxococcus xanthus; Biofilms; Cell Differentiation
PubMed: 37747885
DOI: 10.1128/msystems.00425-23 -
Frontiers in Microbiology 2022Myxobacteria are recognized for fascinating social behaviors and producing diverse extracellular active substances. Isolating novel myxobacteria is of great interest in...
Myxobacteria are recognized for fascinating social behaviors and producing diverse extracellular active substances. Isolating novel myxobacteria is of great interest in the exploitation of new antibiotics and extracellular enzymes. Herein, four novel strains were isolated from Dinghu Mountain Biosphere Reserve, Guangdong province, and Qinghai virgin forest soils, Qinghai province, China. The phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that the four strains belong to the genera and , sharing the highly similarities of 16S rRNA gene with the genera and (99.3-99.6%, respectively). The four strains had average nucleotide identity (ANI) values of 82.8-94.5%, digital DNA-DNA hybridization (dDDH) values of 22.2-56.6%, average amino acid identity (AAI) values of 75.8-79.1% and percentage of conserved protein (POCP) values of 66.4-74.9% to members of the genera and . Based on phylogenetic analyses, physiological and biochemical characteristics, and comparative genomic analyses, we propose four novel species of the genera and and further supported the two genera above represented the same genus. Description of the four novel species is sp. nov. (K38C18041901 = GDMCC 1.2320 = JCM 39260), sp. nov. (QH3KD-4-1 = GDMCC 1.2316 = JCM 39262), sp. nov. (K15C18031901 = GDMCC 1.2319 = JCM 39259), and sp. nov. (QH1ED-7-1 = GDMCC 1.2315 = JCM 39261), respectively. Furthermore, comparative genomics of all 15 species of the genera and revealed extensive genetic diversity. Core genomes enriched more genes associated with housekeeping functional classes while accessory genomes enriched more genes related to environmental interactions, indicating the former is relatively indispensable compared to signaling pathway genes. The 15 species of and also exhibited great gene diversity of carbohydrate-active enzymes (CAZymes) and secondary metabolite biosynthesis gene clusters (BGCs), especially related to glycosyl transferases (GT2 and GT4), glycoside hydrolases (GH13 and GH23), non-ribosomal peptide synthetases (NRPS), and Type I polyketide synthase (PKS)/NRPS hybrids.
PubMed: 36439860
DOI: 10.3389/fmicb.2022.995049 -
Current Opinion in Cell Biology Feb 2020In bacteria, cell polarization involves the controlled targeting of specific proteins to the poles, defining polar identity and function. How a specific protein is... (Review)
Review
In bacteria, cell polarization involves the controlled targeting of specific proteins to the poles, defining polar identity and function. How a specific protein is targeted to one pole and what are the processes that facilitate its dynamic relocalization to the opposite pole is still unclear. The Myxococcus xanthus polarization example illustrates how the dynamic and asymmetric localization of polar proteins enable a controlled and fast switch of polarity. In M. xanthus, the opposing polar distribution of the small GTPase MglA and its cognate activating protein MglB defines the direction of movement of the cell. During a reversal event, the switch of direction is triggered by the Frz chemosensory system, which controls polarity reversals through a so-called gated relaxation oscillator. In this review, we discuss how this genetic architecture can provoke sharp behavioral transitions depending on Frz activation levels, which is central to multicellular behaviors in this bacterium.
Topics: Bacteria; Bacterial Proteins; Cell Polarity; Humans
PubMed: 31627169
DOI: 10.1016/j.ceb.2019.09.001 -
Journal of Bacteriology Nov 2021Myxococcus xanthus is a bacterium that lives on surfaces as a predatory biofilm called a swarm. As a growing swarm feeds on prey and expands, it displays dynamic...
Myxococcus xanthus is a bacterium that lives on surfaces as a predatory biofilm called a swarm. As a growing swarm feeds on prey and expands, it displays dynamic multicellular patterns such as traveling waves called ripples and branching protrusions called flares. The rate at which a swarm expands across a surface, and the emergence of the coexisting patterns, are all controlled through coordinated cell movement. M. xanthus cells move using two motility systems known as adventurous (A) and social (S). Both are involved in swarm expansion and pattern formation. In this study, we describe a set of M. xanthus swarming genotype-to-phenotype associations that include both genetic and environmental perturbations. We identified new features of the swarming phenotype, recorded and measured swarm expansion using time-lapse microscopy, and compared the impact of mutations on different surfaces. These observations and analyses have increased our ability to discriminate between swarming phenotypes and provided context that allows us to identify some phenotypes as improbable outliers within the M. xanthus swarming phenome. Myxococcus xanthus grows on surfaces as a predatory biofilm called a swarm. In nature, a feeding swarm expands by moving over and consuming prey bacteria. In the laboratory, a swarm is created by spotting cell suspension onto nutrient agar in lieu of prey. The suspended cells quickly settle on the surface as the liquid is absorbed into the agar, and the new swarm then expands radially. An assay that measures the expansion rate of a swarm of mutant cells is the first, and sometimes only, measurement used to decide whether a particular mutation impacts swarm motility. We have broadened the scope of this assay by increasing the accuracy of measurements and introducing prey, resulting in new identifiable and quantifiable features that can be used to improve genotype-to-phenotype associations.
Topics: Bacterial Proteins; Bacteriological Techniques; Biofilms; Culture Media; Gene Expression Regulation, Bacterial; Movement; Mutation; Myxococcus xanthus
PubMed: 34543101
DOI: 10.1128/JB.00306-21 -
Journal of Structural Biology Dec 2023Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and...
Encapsulins are self-assembling protein nanocompartments able to selectively encapsulate dedicated cargo enzymes. Encapsulins are widespread across bacterial and archaeal phyla and are involved in oxidative stress resistance, iron storage, and sulfur metabolism. Encapsulin shells exhibit icosahedral geometry and consist of 60, 180, or 240 identical protein subunits. Cargo encapsulation is mediated by the specific interaction of targeting peptides or domains, found in all cargo proteins, with the interior surface of the encapsulin shell during shell self-assembly. Here, we report the 2.53 Å cryo-EM structure of a heterologously produced and highly cargo-loaded T3 encapsulin shell from Myxococcus xanthus and explore the systems' structural heterogeneity. We find that exceedingly high cargo loading results in the formation of substantial amounts of distorted and aberrant shells, likely caused by a combination of unfavorable steric clashes of cargo proteins and shell conformational changes. Based on our cryo-EM structure, we determine and analyze the targeting peptide-shell binding mode. We find that both ionic and hydrophobic interactions mediate targeting peptide binding. Our results will guide future attempts at rationally engineering encapsulins for biomedical and biotechnological applications.
Topics: Bacterial Proteins; Bacteria; Oxidative Stress; Archaea; Peptides
PubMed: 37657675
DOI: 10.1016/j.jsb.2023.108022 -
Biological Chemistry Nov 2020In bacteria, cell-surface polysaccharides fulfill important physiological functions, including interactions with the environment and other cells as well as protection... (Review)
Review
In bacteria, cell-surface polysaccharides fulfill important physiological functions, including interactions with the environment and other cells as well as protection from diverse stresses. The Gram-negative delta-proteobacterium Myxococcus xanthus is a model to study social behaviors in bacteria. M. xanthus synthesizes four cell-surface polysaccharides, i.e., exopolysaccharide (EPS), biosurfactant polysaccharide (BPS), spore coat polysaccharide, and O-antigen. Here, we describe recent progress in elucidating the three Wzx/Wzy-dependent pathways for EPS, BPS and spore coat polysaccharide biosynthesis and the ABC transporter-dependent pathway for O-antigen biosynthesis. Moreover, we describe the functions of these four cell-surface polysaccharides in the social life cycle of M. xanthus.
Topics: Cell Membrane; Myxococcus xanthus; Polysaccharides, Bacterial
PubMed: 32769218
DOI: 10.1515/hsz-2020-0217 -
FEBS Letters Mar 2023Motile cells have developed a large array of molecular machineries to actively change their direction of movement in response to spatial cues from their environment. In... (Review)
Review
Motile cells have developed a large array of molecular machineries to actively change their direction of movement in response to spatial cues from their environment. In this process, small GTPases act as molecular switches and work in tandem with regulators and sensors of their guanine nucleotide status (GAP, GEF, GDI and effectors) to dynamically polarize the cell and regulate its motility. In this review, we focus on Myxococcus xanthus as a model organism to elucidate the function of an atypical small Ras GTPase system in the control of directed cell motility. M. xanthus cells direct their motility by reversing their direction of movement through a mechanism involving the redirection of the motility apparatus to the opposite cell pole. The reversal frequency of moving M. xanthus cells is controlled by modular and interconnected protein networks linking the chemosensory-like frizzy (Frz) pathway - that transmits environmental signals - to the downstream Ras-like Mgl polarity control system - that comprises the Ras-like MglA GTPase protein and its regulators. Here, we discuss how variations in the GTPase interactome landscape underlie single-cell decisions and consequently, multicellular patterns.
Topics: Myxococcus xanthus; Bacterial Proteins; Cell Movement; Signal Transduction; ras Proteins; Multiprotein Complexes; Models, Biological
PubMed: 36520515
DOI: 10.1002/1873-3468.14565