scholarly journals Myxococcus xanthus as a Model Organism for Peptidoglycan Assembly and Bacterial Morphogenesis

2021 ◽  
Author(s):  
Huan Zhang ◽  
Srutha Venkatesan ◽  
Beiyan Nan
Keyword(s):  
De Novo ◽  
Myxococcus Xanthus ◽  
Model Organism ◽  
Life Stages ◽  
Negative Bacterium ◽  
Ideal Model ◽  
Daughter Cells ◽  
Bacterial Division ◽  
Cell Shapes ◽  
Rare Opportunity

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 Myxococcus xanthus 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 M. xanthus 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.

scholarly journals Myxococcus xanthus as a Model Organism for Peptidoglycan Assembly and Bacterial Morphogenesis

2021 ◽  
Vol 9 (5) ◽  
pp. 916
Author(s):  
Huan Zhang ◽  
Srutha Venkatesan ◽  
Beiyan Nan
Keyword(s):  
De Novo ◽  
Myxococcus Xanthus ◽  
Model Organism ◽  
Life Stages ◽  
Negative Bacterium ◽  
Ideal Model ◽  
Daughter Cells ◽  
Bacterial Division ◽  
Cell Shapes ◽  
Rare Opportunity

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 Myxococcus xanthus 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 M. xanthus 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.

scholarly journals Establishing Rod-Shape from Spherical, Peptidoglycan-Deficient Bacterial Spores

2019 ◽  
Author(s):  
Huan Zhang ◽  
Garrett A. Mulholland ◽  
Sofiene Seef ◽  
Shiwei Zhu ◽  
Jun Liu ◽  
...  
Keyword(s):  
Molecular Motors ◽  
De Novo ◽  
Molecular Motor ◽  
Myxococcus Xanthus ◽  
Negative Bacterium ◽  
Gram Negative ◽  
Spherical Surfaces ◽  
Rod System ◽  
The Status ◽  
Ras Family

ABSTRACTChemical-induced spores of the Gram-negative bacterium Myxococcus xanthus are peptidoglycan (PG)-deficient. It is unclear how these spherical spores germinate into rod-shaped, walled cells without preexisting PG templates. We found that germinating spores first synthesize PG randomly on spherical surfaces. MglB, a GTPase-activating protein, forms a cluster that surveys the status of PG growth and stabilizes at one future cell pole. Following MglB, the Ras family GTPase MglA localizes to the second pole. MglA directs molecular motors to transport the bacterial actin homolog MreB and the Rod PG synthesis complexes away from poles. The Rod system establishes rod-shape by elongating PG at nonpolar regions. Thus, the interaction between GTPase, cytoskeletons and molecular motors provides a mechanism for the de novo establishment of rod-shape in bacteria.SignificanceSpheres and rods are among the most common shapes adopted by walled bacteria, in which the peptidoglycan (PG) cell wall largely determines cell shape. When induced by chemicals, rod-shaped vegetative cells of the Gram-negative bacterium Myxococcus xanthus thoroughly degrade their PG and shrink into spherical spores. As these spores germinate, rod-shaped cells are rebuilt without preexisting templates, which provides a rare opportunity to visualize de novo PG synthesis and bacterial morphogenesis. In this study, we investigated how spherical spores germinate into rods and elucidated a system for rod-shape morphogenesis that includes the Rod PG synthesis system, a GTPase-GAP pair, the MreB cytoskeleton and a molecular motor.

scholarly journals Neutral and Phospholipids of the Myxococcus xanthus Lipodome during Fruiting Body Formation and Germination

2015 ◽  
Vol 81 (19) ◽  
pp. 6538-6547 ◽  
Author(s):  
Tilman Ahrendt ◽  
Hendrik Wolff ◽  
Helge B. Bode
Keyword(s):  
Life Cycle ◽  
Lipid Profile ◽  
De Novo ◽  
Membrane Lipids ◽  
Myxococcus Xanthus ◽  
Model Organism ◽  
Ether Lipid ◽  
Complex Life Cycle ◽  
Fruiting Body Formation ◽  
Content Type

ABSTRACTMyxobacteria are well-known for their complex life cycle, including the formation of spore-filled fruiting bodies. The model organismMyxococcus xanthusexhibits a highly complex composition of neutral and phospholipids, including triacylglycerols (TAGs), diacylglycerols (DAGs), phosphatidylethanolamines (PEs), phosphatidylglycerols (PGs), cardiolipins (CLs), and sphingolipids, including ceramides (Cers) and ceramide phosphoinositols (Cer-PIs). In addition, ether lipids have been shown to be involved in development and signaling. In this work, we describe the lipid profile ofM. xanthusduring its entire life cycle, including spore germination. PEs, representing one of the major components of the bacterial membrane, decreased by about 85% during development from vegetative rods to round myxospores, while TAGs first accumulated up to 2-fold before they declined 48 h after the induction of sporulation. Presumably, membrane lipids are incorporated into TAG-containing lipid bodies, serving as an intermediary energy source for myxospore formation. The ceramides Cer(d-19:0/iso-17:0) and Cer(d-19:0/16:0) accumulated 6-fold and 3-fold, respectively, after 24 h of development, identifying them to be novel putative biomarkers forM. xanthussporulation. The most abundant ether lipid, 1-iso-15:0-alkyl-2,3-di-iso-15:0-acyl glycerol (TG1), exhibited a lipid profile different from that of all TAGs during sporulation, reinforcing its signaling character. The absence of all these lipid profile changes in mutants during development supports the importance of lipids in myxobacterial development. During germination of myxospores, only thede novobiosynthesis of new cell membrane fatty acids was observed. The unexpected accumulation of TAGs also during germination might indicate a function of TAGs as intermediary storage lipids during this part of the life cycle as well.

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Lipid Acyl Chain Remodeling in Yeast

2015 ◽  
Vol 8s1 ◽  
pp. LPI.S31780 ◽  
Author(s):  
Mike F. Renne ◽  
Xue Bao ◽  
Cedric H. De Smet ◽  
Anton I. P. M. De Kroon
Keyword(s):  
Intracellular Transport ◽  
De Novo ◽  
Acyl Chain ◽  
Model Organism ◽  
Lipid Synthesis ◽  
Membrane Lipid ◽  
Lipid Homeostasis ◽  
Synthetic Process ◽  
Acyl Chains ◽  
Phospholipid Acyl Chain

Membrane lipid homeostasis is maintained by de novo synthesis, intracellular transport, remodeling, and degradation of lipid molecules. Glycerophospholipids, the most abundant structural component of eukaryotic membranes, are subject to acyl chain remodeling, which is defined as the post-synthetic process in which one or both acyl chains are exchanged. Here, we review studies addressing acyl chain remodeling of membrane glycerophospholipids in Saccharomyces cerevisiae, a model organism that has been successfully used to investigate lipid synthesis and its regulation. Experimental evidence for the occurrence of phospholipid acyl chain exchange in cardiolipin, phosphatidylcholine, phosphatidylinositol, and phosphatidylethanolamine is summarized, including methods and tools that have been used for detecting remodeling. Progress in the identification of the enzymes involved is reported, and putative functions of acyl chain remodeling in yeast are discussed.

scholarly journals Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

2019 ◽  
Author(s):  
Valentina Peona ◽  
Mozes P.K. Blom ◽  
Luohao Xu ◽  
Reto Burri ◽  
Shawn Sullivan ◽  
...  
Keyword(s):  
Dark Matter ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
De Novo ◽  
Model Organism ◽  
Technology Choice ◽  
High Quality ◽  
Sequencing Technologies ◽  
Downstream Analysis ◽  
Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

scholarly journals Parasitic wasps do not lack lipogenesis

2021 ◽  
Author(s):  
Joachim Ruther ◽  
Lorena Prager ◽  
Tamara Pokorny
Keyword(s):  
Fatty Acids ◽  
De Novo ◽  
Model Organism ◽  
Parasitic Wasps ◽  
Primary Metabolites ◽  
De Novo Biosynthesis ◽  
Fat Reserves ◽  
Lipid Mass ◽  
Unlimited Access ◽  
Eleven Species

Fatty acids are crucial primary metabolites for virtually any creature on earth. Therefore, most organisms do not rely exclusively on nutritional supply with fatty acids but have the ability to synthesize fatty acids and triacylglycerides de novo from carbohydrates, a process called lipogenesis. The ubiquity of lipogenesis has been questioned by a series of studies reporting that many parasitic wasps (parasitoids) do not accumulate lipid mass despite having unlimited access to sugar. This has been interpreted as an evolutionary metabolic trait loss in parasitoids. Here, we demonstrate de novo biosynthesis of fatty acids from 13C-labeled α-D-glucose in eleven species of parasitoids from six families. We furthermore show with the model organism Nasonia vitripennis that lipogenesis occurs even when lipid reserves are still intact, but relative 13C-incorporation rates increase in females with widely depleted fat reserves. Therefore, we conclude that the presumed "lack of lipogenesis" in parasitoids needs to be re-evaluated.

scholarly journals Basal-Level Effects of (p)ppGpp in the Absence of Branched-Chain Amino Acids in Actinobacillus pleuropneumoniae

2020 ◽  
Vol 202 (8) ◽  
Author(s):  
Gang Li ◽  
Qian Zhao ◽  
Tian Luan ◽  
Yangbo Hu ◽  
Yueling Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
De Novo ◽  
Model Organism ◽  
Stringent Response ◽  
Actinobacillus Pleuropneumoniae ◽  
Branched Chain Amino Acids ◽  
Content Type ◽  
Phenotypic Differences ◽  
Branched Chain

ABSTRACT The (p)ppGpp-mediated stringent response (SR) is a highly conserved regulatory mechanism in bacterial pathogens, enabling adaptation to adverse environments, and is linked to pathogenesis. Actinobacillus pleuropneumoniae can cause damage to the lungs of pigs, its only known natural host. Pig lungs are known to have a low concentration of free branched-chain amino acids (BCAAs) compared to the level in plasma. We had investigated the role for (p)ppGpp in viability and biofilm formation of A. pleuropneumoniae. Now, we sought to determine whether (p)ppGpp was a trigger signal for the SR in A. pleuropneumoniae in the absence of BCAAs. Combining transcriptome and phenotypic analyses of the wild type (WT) and an relA spoT double mutant [which does not produce (p)ppGpp], we found that (p)ppGpp could repress de novo purine biosynthesis and activate antioxidant pathways. There was a positive correlation between GTP and endogenous hydrogen peroxide content. Furthermore, the growth, viability, morphology, and virulence were altered by the inability to produce (p)ppGpp. Genes involved in the biosynthesis of BCAAs were constitutively upregulated, regardless of the existence of BCAAs, without accumulation of (p)ppGpp beyond a basal level. Collectively, our study shows that the absence of BCAAs was not a sufficient signal to trigger the SR in A. pleuropneumoniae. (p)ppGpp-mediated regulation in A. pleuropneumoniae is different from that described for the model organism Escherichia coli. Further work will establish whether the (p)ppGpp-dependent SR mechanism in A. pleuropneumoniae is conserved among other veterinary pathogens, especially those in the Pasteurellaceae family. IMPORTANCE (p)ppGpp is a key player in reprogramming transcriptomes to respond to nutritional challenges. Here, we present transcriptional and phenotypic differences of A. pleuropneumoniae grown in different chemically defined media in the absence of (p)ppGpp. We show that the deprivation of branched-chain amino acids (BCAAs) does not elicit a change in the basal-level (p)ppGpp, but this level is sufficient to regulate the expression of BCAA biosynthesis. The mechanism found in A. pleuropneumoniae is different from that of the model organism Escherichia coli but similar to that found in some Gram-positive bacteria. This study not only broadens the research scope of (p)ppGpp but also further validates the complexity and multiplicity of (p)ppGpp regulation in microorganisms that occupy different biological niches.

scholarly journals The carbonate concentration mechanism of Pyropia yezoensis (Rhodophyta): evidence from transcriptomics and biochemical data

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Baoyu Zhang ◽  
Xiujun Xie ◽  
Xuehua Liu ◽  
Linwen He ◽  
Yuanyuan Sun ◽  
...  
Keyword(s):  
Photosynthetic Efficiency ◽  
Inorganic Carbon ◽  
De Novo ◽  
Isocitrate Lyase ◽  
Life Cycles ◽  
Malate Synthase ◽  
Pyropia Yezoensis ◽  
Cdna Libraries ◽  
Life Stages ◽  
Low Carbon

Abstract Background Pyropia yezoensis (Rhodophyta) is widely cultivated in East Asia and plays important economic, ecological and research roles. Although inorganic carbon utilization of P. yezoensis has been investigated from a physiological aspect, the carbon concentration mechanism (CCM) of P. yezoensis remains unclear. To explore the CCM of P. yezoensis, especially during its different life stages, we tracked changes in the transcriptome, photosynthetic efficiency and in key enzyme activities under different inorganic carbon concentrations. Results Photosynthetic efficiency demonstrated that sporophytes were more sensitive to low carbon (LC) than gametophytes, with increased photosynthesis rate during both life stages under high carbon (HC) compared to normal carbon (NC) conditions. The amount of starch and number of plastoglobuli in cells corresponded with the growth reaction to different inorganic carbon (Ci) concentrations. We constructed 18 cDNA libraries from 18 samples (three biological replicates per Ci treatment at two life cycles stages) and sequenced these using the Illumina platform. De novo assembly generated 182,564 unigenes, including approximately 275 unigenes related to CCM. Most genes encoding internal carbonic anhydrase (CA) and bicarbonate transporters involved in the biophysical CCM pathway were induced under LC in comparison with NC, with transcript abundance of some PyCAs in gametophytes typically higher than that in sporophytes. We identified all key genes participating in the C4 pathway and showed that their RNA abundances changed with varying Ci conditions. High decarboxylating activity of PEPCKase and low PEPCase activity were observed in P. yezoensis. Activities of other key enzymes involved in the C4-like pathway were higher under HC than under the other two conditions. Pyruvate carboxylase (PYC) showed higher carboxylation activity than PEPC under these Ci conditions. Isocitrate lyase (ICL) showed high activity, but the activity of malate synthase (MS) was very low. Conclusion We elucidated the CCM of P. yezoensis from transcriptome and enzyme activity levels. All results indicated at least two types of CCM in P. yezoensis, one involving CA and an anion exchanger (transporter), and a second, C4-like pathway belonging to the PEPCK subtype. PYC may play the main carboxylation role in this C4-like pathway, which functions in both the sporophyte and gametophyte life cycles.

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