Analysis of the Spore Membrane Proteome in Clostridium perfringens Implicates Cyanophycin in Spore Assembly

Cyanophycin and its biosynthesis: not hot but very cool

Covering: 1878 to early 2023Cyanophycin is a biopolymer consisting of a poly-aspartate backbone with arginines linked to each Asp sidechain through isopeptide bonds. Cyanophycin is made by cyanophycin synthetase 1 or 2 through ATP-dependent polymerization of Asp and Arg, or β-Asp-Arg, respectively. It is degraded into dipeptides by exo-cyanophycinases, and these dipeptides are hydrolyzed into free amino acids by general or dedicated isodipeptidase enzymes. When synthesized, chains of cyanophycin coalesce into large, inert, membrane-less granules. Although discovered in cyanobacteria, cyanophycin is made by species throughout the bacterial kingdom, and cyanophycin metabolism provides advantages for toxic bloom forming algae and some human pathogens. Some bacteria have developed dedicated schemes for cyanophycin accumulation and use, which include fine temporal and spatial regulation. Cyanophycin has also been heterologously produced in a variety of host organisms to a remarkable level, over 50% of the host's dry mass, and has potential for a variety of green industrial applications. In this review, we summarize the progression of cyanophycin research, with an emphasis on recent structural studies of enzymes in the cyanophycin biosynthetic pathway. These include several unexpected revelations that show cyanophycin synthetase to be a very cool, multi-functional macromolecular machine.

Structures and function of the amino acid polymerase cyanophycin synthetase

Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide bonds. Cyanophycin is synthesized from ATP, aspartic acid and arginine by a homooligomeric enzyme called cyanophycin synthetase (CphA1). CphA1 has domains that are homologous to glutathione synthetases and muramyl ligases, but no other structural information has been available. Here, we present cryo-electron microscopy and X-ray crystallography structures of cyanophycin synthetases from three different bacteria, including cocomplex structures of CphA1 with ATP and cyanophycin polymer analogs at 2.6 Å resolution. These structures reveal two distinct tetrameric architectures, show the configuration of active sites and polymer-binding regions, indicate dynamic conformational changes and afford insight into catalytic mechanism. Accompanying biochemical interrogation of substrate binding sites, catalytic centers and oligomerization interfaces combine with the structures to provide a holistic understanding of cyanophycin biosynthesis.

Functional Characterization of Primordial Protein Repair Enzyme M38 Metallo-Peptidase From Fervidobacterium islandicum AW-1

The NA23_RS08100 gene of Fervidobacterium islandicum AW-1 encodes a keratin-degrading β-aspartyl peptidase (FiBAP) that is highly expressed under starvation conditions. Herein, we expressed the gene in Escherichia coli, purified the recombinant enzyme to homogeneity, and investigated its function. The 318 kDa recombinant FiBAP enzyme exhibited maximal activity at 80°C and pH 7.0 in the presence of Zn²⁺. Size-exclusion chromatography revealed that the native enzyme is an octamer comprising a tetramer of dimers; this was further supported by determination of its crystal structure at 2.6 Å resolution. Consistently, the structure of FiBAP revealed three additional salt bridges in each dimer, involving 12 ionic interactions that might contribute to its high thermostability. In addition, the co-crystal structure containing the substrate analog N-carbobenzoxy-β-Asp-Leu at 2.7 Å resolution revealed binuclear Zn²⁺-mediated substrate binding, suggesting that FiBAP is a hyperthermophilic type-I IadA, in accordance with sequence-based phylogenetic analysis. Indeed, complementation of a Leu auxotrophic E. coli mutant strain (ΔiadA and ΔleuB) with FiBAP enabled the mutant strain to grow on isoAsp-Leu peptides. Remarkably, LC-MS/MS analysis of soluble keratin hydrolysates revealed that FiBAP not only cleaves the C-terminus of isoAsp residues but also has a relatively broad substrate specificity toward α-peptide bonds. Moreover, heat shock-induced protein aggregates retarded bacterial growth, but expression of BAP alleviated the growth defect by degrading damaged proteins. Taken together, these results suggest that the viability of hyperthermophiles under stressful conditions may rely on the activity of BAP within cellular protein repair systems.

Fecal Metaproteomic Analysis Reveals Unique Changes of the Gut Microbiome Functions After Consumption of Sourdough Carasau Bread

Sourdough-leavened bread (SB) is acknowledged for its great variety of valuable effects on consumer's metabolism and health, including a low glycemic index and a reduced content of the possible carcinogen acrylamide. Here, we aimed to investigate how these effects influence the gut microbiota composition and functions. Therefore, we subjected rats to a diet supplemented with SB, baker's yeast leavened bread (BB), or unsupplemented diet (chow), and, after 4 weeks of treatment, their gut microbiota was analyzed using a metaproteogenomic approach. As a result, diet supplementation with SB led to a reduction of specific members of the intestinal microbiota previously associated to low protein diets, namely Alistipes and Mucispirillum, or known as intestinal pathobionts, i.e., Mycoplasma. Concerning functions, asparaginases expressed by Bacteroides were observed as more abundant in SB-fed rats, leading to hypothesize that in their colonic microbiota the enzyme substrate, asparagine, was available in higher amounts than in BB- and chow-fed rats. Another group of protein families, expressed by Clostridium, was detected as more abundant in animal fed SB-supplemented diet. Of these, manganese catalase, small acid-soluble proteins (SASP), Ser/Thr kinase PrkA, and V-ATPase proteolipid subunit have been all reported to take part in Clostridium sporulation, strongly suggesting that the diet supplementation with SB might promote environmental conditions inducing metabolic dormancy of Clostridium spp. within the gut microbiota. In conclusion, our data describe the effects of SB consumption on the intestinal microbiota taxonomy and functions in rats. Moreover, our results suggest that a metaproteogenomic approach can provide evidence of the interplay between metabolites deriving from bread digestion and microbial metabolism.

Microbial production of cyanophycin: From enzymes to biopolymers

Cyanophycin is an attractive biopolymer with chemical and material properties that are suitable for industrial applications in the fields of food, medicine, cosmetics, nutrition, and agriculture. For efficient production of cyanophycin, considerable efforts have been exerted to characterize cyanophycin synthetases (CphAs) and optimize fermentations and downstream processes. In this paper, we review the characteristics of diverse CphAs from cyanobacteria and non-cyanobacteria. Furthermore, strategies for cyanophycin production in microbial strains, including Escherichia coli, Pseudomonas putida, Ralstonia eutropha, Rhizopus oryzae, and Saccharomyces cerevisiae, heterologously expressing different cphA genes are reviewed. Additionally, chemical and material properties of cyanophycin and its derivatives produced through biological or chemical modifications are reviewed in the context of their industrial applications. Finally, future perspectives on microbial production of cyanophycin are provided to improve its cost-effectiveness.

"One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores

PURPOSE

Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against a variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles.

EXPERIMENTAL DESIGN

The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead beating in 6 m urea under reductive conditions. The heterogeneous mixture was then double digested with LysC and trypsin. Next, the peptide mixture was pre-fractionated with zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) followed by reverse-phase LC-FT-MS analysis of the fractions.

RESULTS

"One-pot" method is a simple, robust method that yields identification of >1000 proteins with high confidence, across all spore layers from B. subtilis, B. cereus, and P. difficile.

CONCLUSIONS AND MEDICAL RELEVANCE

This method can be employed for proteome-wide analysis of non-spore-forming as well as spore-forming pathogens. Analysis of spore protein profile will help to understand the sporulation and germination processes and to distinguish immunogenic protein markers.

Complete Genome Sequence of Bacillus horikoshii Strain 20a from Cuatro Cienegas, Coahuila, Mexico

We sequenced the Bacillus horikoshii 20a genome, isolated from sediment collected in Cuatro Cienegas, Mexico. We identified genes involved in establishing antagonistic interactions in microbial communities (antibiotic resistance and bacteriocins) and genes related to the metabolism of cyanophycin, a reserve compound and spore matrix material potentially relevant for survival in an oligotrophic environment.

Germination of Spores of the Orders Bacillales and Clostridiales

Dormant Bacillales and Clostridiales spores begin to grow when small molecules (germinants) trigger germination, potentially leading to food spoilage or disease. Germination-specific proteins sense germinants, transport small molecules, and hydrolyze specific bonds in cortex peptidoglycan and specific proteins. Major events in germination include (a) germinant sensing; (b) commitment to germinate; (c) release of spores' depot of dipicolinic acid (DPA); (d) hydrolysis of spores' peptidoglycan cortex; and (e) spore core swelling and water uptake, cell wall peptidoglycan remodeling, and restoration of core protein and inner spore membrane lipid mobility. Germination is similar between Bacillales and Clostridiales, but some species differ in how germinants are sensed and how cortex hydrolysis and DPA release are triggered. Despite detailed knowledge of the proteins and signal transduction pathways involved in germination, precisely what some germination proteins do and how they do it remain unclear.

Characterization of germinants and their receptors for spores of non-food-borne Clostridium perfringens strain F4969

Clostridium perfringens type A can cause both food poisoning (FP) and non-food-borne (NFB) gastrointestinal diseases. Our previous study reported that a mixture of l-asparagine and KCl (AK)-germinated spores of FP and NFB isolates well, but KCl and, to a lesser extent, l-asparagine induced spore germination only in FP isolates. We now report that the germination response of FP and NFB spores differsignificantly in several defined germinants and rich media. Spores of NFB strain F4969 gerAA, gerKA-KC or gerKC mutants lacking specific germinant receptor proteins germinated more slowly than wild-type spores with rich media, did not germinate with AK and germinated poorly compared to wild-type spores with l-cysteine. The germination defects in the gerKA-KC spores were largely due to loss of GerKC as (i) gerKA spores germinated significantly with all tested germinants, while gerKC spores exhibited poor or no germination; and (ii) germination defects in gerKC spores were largely restored by expressing the wild-type gerKA-KC operon in trans. We also found that gerKA-KC, gerAA and gerKC spores, but not gerKA spores, released dipicolinic acid at a slower rate than wild-type spores with AK. The colony-forming efficiency of F4969 gerKC spores was also ~35-fold lower than that of wild-type spores, while gerAA and wild-type spores had similar viability. Collectively, these results suggest that the GerAA and GerKC proteins play roles in normal germination of C. perfringens NFB isolates and that GerKC, but not GerAA, is important in these spores' apparent viability.