Reconstitution of a minimal motility system based on Spiroplasma swimming by two bacterial actins in a synthetic minimal bacterium

Robust and highly efficient transformation method for a minimal mycoplasma cell

Mycoplasmas have been widely investigated for their pathogenicity, as well as for genomics and synthetic biology. Conventionally, transformation of mycoplasmas was not highly efficient, and due to the low transformation efficiency, large amounts of DNA and recipient cells were required for that purpose. Here, we report a robust and highly efficient transformation method for the minimal cell JCVI-syn3B, which was created through streamlining the genome of Mycoplasma mycoides. When the growth states of JCVI-syn3B were examined in detail by focusing on such factors as pH, color, absorbance, colony forming unit, and transformation efficiency, it was found that the growth phase after the lag phase can be divided into three distinct phases, of which the highest transformation efficiency was observed during the early exponential growth phase. Notably, the transformation efficiency of up to 4.4 × 10-2 transformants per cell per microgram of plasmid DNA was obtained. A method to obtain several hundred to several thousand transformants with less than 0.2 mL of culture with approximately 1 × 107-108 cells and 10 ng of plasmid DNA was developed. Moreover, a transformation method using a frozen stock of transformation-ready cells was established. These procedures and information could simplify and enhance the transformation process of minimal cells, facilitating advanced genetic engineering and biological research using minimal cells.

IMPORTANCE

Mycoplasmas are parasitic and pathogenic bacteria for many animals. They are also useful bacteria to understand the cellular process of life and for bioengineering because of their simple metabolism, small genomes, and cultivability. Genetic manipulation is crucial for these purposes, but transformation efficiency in mycoplasmas is typically quite low. Here, we report a highly efficient transformation method for the minimal genome mycoplasma JCVI-syn3B. Using this method, transformants can be obtained with only 10 ng of plasmid DNA, which is around one-thousandth of the amount required for traditional mycoplasma transformations. Moreover, a convenient method using frozen stocks of transformation-ready cells was established. These improved methods play a crucial role in further studies using minimal cells.

Rapid in vitro method to assemble and transfer DNA fragments into the JCVI-syn3B minimal synthetic bacterial genome through Cre/loxP system

JCVI-syn3B (syn3B), a minimal synthetic bacterium that only possesses essential genes, facilitates the examination of heterogeneous gene functions in minimal life. Conventionally, Escherichia coli is used to construct DNA fragments for gene transfer into the syn3B genome through Cre/loxP system. However, the construction process is challenging and time-consuming due to various issues, including the inhibition of E. coli growth and unexpected recombination, especially with AT-rich DNA sequences such as those found in Mycoplasma genes. Therefore, in this study, we aimed to develop a new transformation method to overcome these issues. We assembled the vector and target DNA fragments using an in vitro homologous recombination system and subsequently transferred the products into the syn3B genome. We obtained approximately 103~104 recombinant colonies per milliliter of the original culture in eight days, which is four days shorter than the conventional period, without any recombination issues, even for AT-rich DNA. This method may be applicable to other gene manipulation systems based on Cre/loxP system.

Deciphering the impact of MreB on the morphology and pathogenicity of the aquatic pathogen Spiroplasma eriocheiris

BACKGROUND

Spiroplasma eriocheiris has been proved to be a pathogen causing tremor disease of Eriocheir sinensis, it is also infectious to other aquatic crustaceans, resulting in a serious threat on the sustainable development of the aquaculture industry. S. eriocheiris is a helical-shaped microbe without a cell wall, and its motility is related to the cytoskeleton protein MreB which belongs to the actin superfamily and has five MreB homologs.

RESULTS

In this study, we purified MreB3, MreB4 and MreB5, and successfully prepared monoclonal antibodies. After S. eriocheiris treated with actin stabilizator Phalloidin and inhibitors A22, we found that Phalloidin and A22 affect the S. eriocheiris morphology by altering MreB expression. We confirmed that the ability of S. eriocheiris to invade E. sinensis was increased after treatment with Phalloidin, including that the morphology of E. sinensis blood lymphocytes was deteriorated, blood lymphocytes viability was decreased, peroxidase activity and cell necrosis were increased. On the contrary, the pathogenicity of S. eriocheiris decreased after treatment with A22.

CONCLUSIONS

Our findings suggest that the MreB protein in S. eriocheiris plays a crucial role in its morphology and pathogenicity, providing new insights into potential strategies for the prevention and control of S. eriocheiris infections.

Integrated Information for Pathogenicity and Treatment of Spiroplasma

Spiroplasma, belonging to the class Mollicutes, is a small, helical, motile bacterium lacking a cell wall. Its host range includes insects, plants, and aquatic crustaceans. Recently, a few human cases of Spiroplasma infection have been reported. The diseases caused by Spiroplasma have brought about serious economic losses and hindered the healthy development of agriculture. The pathogenesis of Spiroplasma involves the ability to adhere, such as through the terminal structure of Spiroplasma, colonization, and invasive enzymes. However, the exact pathogenic mechanism of Spiroplasma remains a mystery. Therefore, we systematically summarize all the information about Spiroplasma in this review article. This provides a reference for future studies on virulence factors and treatment strategies of Spiroplasma.

Cloning and sequencing analysis of whole Spiroplasma genome in yeast

Cloning and transfer of long-stranded DNA in the size of a bacterial whole genome has become possible by recent advancements in synthetic biology. For the whole genome cloning and whole genome transplantation, bacteria with small genomes have been mainly used, such as mycoplasmas and related species. The key benefits of whole genome cloning include the effective maintenance and preservation of an organism's complete genome within a yeast host, the capability to modify these genome sequences through yeast-based genetic engineering systems, and the subsequent use of these cloned genomes for further experiments. This approach provides a versatile platform for in-depth genomic studies and applications in synthetic biology. Here, we cloned an entire genome of an insect-associated bacterium, Spiroplasma chrysopicola, in yeast. The 1.12 Mbp whole genome was successfully cloned in yeast, and sequences of several clones were confirmed by Illumina sequencing. The cloning efficiency was high, and the clones contained only a few mutations, averaging 1.2 nucleotides per clone with a mutation rate of 4 × 10-6. The cloned genomes could be distributed and used for further research. This study serves as an initial step in the synthetic biology approach to Spiroplasma.

The Lithbea Domain

The tree of life is the evolutionary metaphor for the past and present connections of all cellular organisms. Today, to speak of biodiversity is not only to speak of archaea, bacteria, and eukaryotes, but they should also consider the "new biodiversity" that includes viruses and synthetic organisms, which represent the new forms of life created in laboratories. There is even a third group of artificial entities that, although not living systems, pretend to imitate the living. To embrace and organize all this new biodiversity, I propose the creation of a new domain, with the name Lithbea (from life-on-the-border entites) The criteria for inclusion as members of Lithbea are: i) the acellular nature of the living system, ii) its origin in laboratory manipulation, iii) showing new biological traits, iv) the presence of exogenous genetic elements, v) artificial or inorganic nature. Within Lithbea there are two subdomains: Virworld (from virus world) which includes all viruses, regarded as lifeless living systems, and classified according to the International Committee on Taxonomy of Viruses (ICTV), and ii) Humade (from human-made) which includes all synthetic organisms and artificial entities. The relationships of Lithbea members to the three classical woesian domains and their implications are briefly discussed.

Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities

The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.

iTRAQ-based differential proteomic analysis of high- and low-virulence strains of Spiroplasma eriocheiris

Spiroplasma eriocheiris is one of the major pathogenic bacteria in crustaceans, featuring high infectivity, rapid transmission, and an absence of effective control strategies, resulting in significant economic losses to the aquaculture industry. Research into virulence-related factors provides an important perspective to clarify how Spiroplasma eriocheiris is pathogenic to shrimps and crabs. Therefore, in this study, isobaric tags for relative and absolute quantitation (iTRAQ) technology was utilized to undertake a differential proteomic analysis of high- and low-virulence Spiroplasma eriocheiris strains at different growth phases. A total of 868 differentially expressed proteins (DEPs) were obtained, of which 31 novel proteins were identified by proteogenomic analysis. There were 62, 61, 175, and 235 DEPs between the log phase (YD) and non-log phase (YFD) of the high-virulence strain, between the log phase (CD) and non-log phase (CFD) of the low-virulence strain, between YD and CD, and between CFD and YFD, respectively. All the DEPs were compared with virulence protein databases (MvirDB and VFDB), and 68 virulence proteins of Spiroplasma eriocheiris were identified, of which 12 were involved in a total of 21 metabolic pathways, including motility, chemotaxis, growth, metabolism and virulence of the bacteria. The results of this study form the basis for further research into the molecular mechanism of virulence and physiological differences between high- and low-virulence strains of Spiroplasma eriocheiris, and provide a scientific basis for a detailed understanding of its pathogenesis.

Bend or Twist? What Plectonemes Reveal about the Mysterious Motility of Spiroplasma

Spiroplasma is a unique, helical bacterium that lacks a cell wall and swims using propagating helix hand inversions. These deformations are likely driven by a set of cytoskeletal filaments, but how remains perplexing. Here, we probe the underlying mechanism using a model where either twist or bend drive spiroplasma's chirality inversions. We show that Spiroplasma should wrap into plectonemes at different values of the length and external viscosity, depending on the mechanism. Then, by experimentally measuring the bending modulus of Spiroplasma and if and when plectonemes form, we show that Spiroplasma's helix hand inversions are likely driven by bending.

Rheotaxis in Mycoplasma gliding

This review describes the upstream-directed movement in the small parasitic bacterium Mycoplasma. Many Mycoplasma species exhibit gliding motility, a form of biological motion over surfaces without the aid of general surface appendages such as flagella. The gliding motility is characterized by a constant unidirectional movement without changes in direction or backward motion. Unlike flagellated bacteria, Mycoplasma lacks the general chemotactic signaling system to control their moving direction. Therefore, the physiological role of directionless travel in Mycoplasma gliding remains unclear. Recently, high-precision measurements under an optical microscope have revealed that three species of Mycoplasma exhibited rheotaxis, that is, the direction of gliding motility is lead upstream by the water flow. This intriguing response appears to be optimized for the flow patterns encountered at host surfaces. This review provides a comprehensive overview of the morphology, behavior, and habitat of Mycoplasma gliding, and discusses the possibility that the rheotaxis is ubiquitous among them.

Assembly properties of Spiroplasma MreB involved in swimming motility

Bacterial actin MreB forms filaments formed of antiparallel double strand units. The wall-less helical bacterium Spiroplasma has five MreB homologs (MreB1-5), some of which are involved in an intra-cellular ribbon for driving the bacterium's swimming motility. Although the interaction between MreB units is important for understanding Spiroplasma swimming, the interaction modes of each ribbon component are unclear. Here, we examined the assembly properties of Spiroplasma eriocheiris MreB5 (SpeMreB5), one of the ribbon component proteins that forms sheets. Electron microscopy (EM) revealed that sheet formation was inhibited under acidic conditions and bundle structures were formed under acidic and neutral conditions with low ionic strength. We also used solution assays and identified four properties of SpeMreB5 bundles as follows: (I) bundle formation followed sheet formation; (II) electrostatic interactions were required for bundle formation; (III) the positively charged and unstructured C-terminal region contributed to promoting lateral interactions for bundle formation; and (IV) bundle formation required Mg²⁺ at neutral pH but was inhibited by divalent cations under acidic pH conditions. During these studies, we also characterized two aggregation modes of SpeMreB5 with distinct responses to ATP. These properties will shed light on SpeMreB5 assembly dynamics at the molecular level.

Swimming Motility Assays of Spiroplasma

Spiroplasma swim in liquids without the use of the bacterial flagella. This small helical bacterium propels itself by generating kinks that travel down the cell body. The kink translation is unidirectional, from the leading pole to the lagging pole, during cell swimming in viscous environments. This protocol describes a swimming motility assay of Spiroplasma eriocheiris for visualizing kink translations of the absolute handedness of the body helix with optical microscopy.

Purification and ATPase Activity Measurement of Spiroplasma MreB

Spiroplasma is a genus of wall-less helical bacteria with swimming motility unrelated to conventional types of bacterial motility machinery, such as flagella and pili. The swimming of Spiroplasma is suggested to be driven by five classes of MreB (MreB1-MreB5), which are members of the actin superfamily. In vitro studies of Spiroplasma MreBs have recently been conducted to evaluate their activities, such as ATPase, which is essential for the polymerization dynamics among classic actin superfamily proteins. In this chapter, we describe methods of purification and P_i release measurement of Spiroplasma MreBs using column chromatography and absorption spectroscopy with the molecular probe, 2-amino-6-mercapto-7-methylpurine riboside (MESG). Of note, the methods described here are applicable to other proteins that possess NTPase activity.

Sequence analyses of a lipoprotein conserved with bacterial actins responsible for swimming motility of wall-less helical Spiroplasma

Spiroplasma is a genus of pathogenic or commensal cell-wall-deficient helical bacterium. Spiroplasma -specific protein fibril and five classes of bacterial actins, MreB1-5, are involved in a helical ribbon structure responsible for helical-cell morphology and swimming motility. A gene for a hypothetical protein-SPE_1229, 7th protein-has been found in the locus coding mreB s. In this study, we characterized the 7th protein using in silico methods and found that it could be a lipoprotein whose gene is encoded downstream of mreB3 and conserved in a clade of Spiroplasma .