Characterization of an AA9 LPMO from Thielavia australiensis, TausLPMO9B, under industrially relevant lignocellulose saccharification conditions

BACKGROUND

The discovery of lytic polysaccharide monooxygenases (LPMO) has changed our perspective on enzymatic degradation of plant biomass. Through an oxidative mechanism, these enzymes are able to cleave and depolymerize various polysaccharides, acting not only on crystalline substrates such as chitin and cellulose, but also on other polysaccharides, such as xyloglucan, glucomannan and starch. Despite their widespread use, uncertainties related to substrate specificity and stereospecificity, the nature of the co-substrate, in-process stability, and the nature of the optimal reductant challenge their exploitation in biomass processing applications.

RESULTS

In this work, we studied the properties of a novel fungal LPMO from the thermophilic fungus Thielavia australiensis, TausLPMO9B. Heterologous expression of TausLPMO9B in Aspergillus niger yielded a glycosylated protein with a methylated N-terminal histidine showing LPMO activity. High sequence identity of the AA9 domain to that of MtLPMO9B (MYCTH_80312) from Myceliophthora thermophila (84%) indicated strictly C1-oxidizing activity on cellulose, which was confirmed experimentally by the analysis of products released from cellulose using HPAEC. The enzyme was stable and active at a pH ranging from 4 to 6, thus matching the conditions commonly used in industrial biomass processing, where a low pH (between 4 and 5) is used due to the pH-optima of commercial cellulases and a desire to limit microbial contamination.

CONCLUSION

While the oxidative cleavage of phosphoric acid swollen cellulose (PASC) by TausLPMO9B was boosted by the addition of H₂O₂ as a co-substrate, this effect was not observed during the saccharification of acid pretreated corn stover. This illustrates key differences between the lab-scale tests with artificial, lignin-free substrates and industrial settings with lignocellulosic biomass as substrate.

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system

BACKGROUND

In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa.

RESULTS

The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from Ca. P. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected Ca. P. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage β-glucans.

CONCLUSION

We propose that Ca. P. polyenzymogene genotypes and other Ca. MH11 members actively degrade plant biomass in the rumen of cows, sheep and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.

Display of recombinant proteins at the surface of lactic acid bacteria: strategies and applications

Lactic acid bacteria (LAB) are promising vectors of choice to deliver active molecules to mucosal tissues. They are recognized as safe by the World Health Organization and some strains have probiotic properties. The wide range of potential applications of LAB-driven mucosal delivery includes control of inflammatory bowel disease, vaccine delivery, and management of auto-immune diseases. Because of this potential, strategies for the display of proteins at the surface of LAB are gaining interest. To display a protein at the surface of LAB, a signal peptide and an anchor domain are necessary. The recombinant protein can be attached to the membrane layer, using a transmembrane anchor or a lipoprotein-anchor, or to the cell wall, by a covalent link using sortase mediated anchoring via the LPXTG motif, or by non-covalent liaisons employing binding domains such as LysM or WxL. Both the stability and functionality of the displayed proteins will be affected by the kind of anchor used. The most commonly surfaced exposed recombinant proteins produced in LAB are antigens and antibodies and the most commonly used LAB are lactococci and lactobacilli. Although it is not necessarily so that surface-display is the preferred localization in all cases, it has been shown that for certain applications, such as delivery of the human papillomavirus E7 antigen, surface-display elicits better biological responses, compared to cytosolic expression or secretion. Recent developments include the display of peptides and proteins targeting host cell receptors, for the purpose of enhancing the interactions between LAB and host. Surface-display technologies have other potential applications, such as degradation of biomass, which is of importance for some potential industrial applications of LAB.

Experimental and computational analysis of the secretome of the hyperthermophilic archaeon Pyrococcus furiosus

Although Pyrococcus furiosus is one of the best studied hyperthermophilic archaea, to date no experimental investigation of the extent of protein secretion has been performed. We describe experimental verification of the extracellular proteome of P. furiosus grown on starch. LC-MS/MS-based analysis of culture supernatants led to the identification of 58 proteins. Fifteen of these proteins had a putative N-terminal signal peptide (SP), tagging the proteins for translocation across the membrane. The detected proteins with predicted SPs and known function were almost exclusively involved in important extracellular functions, like substrate degradation or transport. Most of the 43 proteins without predicted N-terminal signal sequences are known to have intracellular functions, mainly (70 %) related to intracellular metabolism. In silico analyses indicated that the genome of P. furiosus encodes 145 proteins with N-terminal SPs, including 21 putative lipoproteins and 17 with a class III peptide. From these we identified 15 (10 %; 7 SPI, 3 SPIII and 5 lipoproteins) under the specific growth conditions of this study. The putative lipoprotein signal peptides have a unique sequence motif, distinct from the motifs in bacteria and other archaeal orders.

The role of calcium ions in the stability and instability of a thermolysin-like protease

Thermolysin and other secreted broad-specificity proteases, such as subtilisin or alpha-lytic protease, are produced as pre-pro-proteins that stay at least partially unfolded while in the cytosol. After secretion, the pro-proteases fold to their active conformations in a process that includes the autolytic removal of the pro-peptide. We review the life cycle of the thermolysin-like protease from Bacillus stearothermophilus in light of the calcium dependent stability and instability of the N-terminal domain. The protease binds calcium ions in the regions that are involved in the autolytic maturation process. It is generally assumed that the calcium ions contribute to the extreme stability of the protease, but experimental evidence for TLP-ste indicates that at least one of the calcium ions plays a regulatory role. We hypothesize that this calcium ion plays an important role as a switch that modulates the protease between stable and unstable states as appropriate to the biological need.

Use of lactobacilli and their pheromone-based regulatory mechanism in gene expression and drug delivery

Lactobacilli are common microorganisms in diverse vegetables and meat products and several of these are also indigenous inhabitants in the gastro-intestinal (GI) tract of humans and animals where they are believed to have health promoting effects on the host. One of the highly appreciated probiotic effects is their ability to inhibit the growth of pathogens by producing antimicrobial peptides, so-called bacteriocins. Production of some bacteriocins has been shown to be strictly regulated through a quorum-sensing based mechanism mediated by a secreted peptide-pheromone (also called induction peptide; IP), a membrane-located sensor (histidine protein kinase; HPK) and a cytoplasmic response regulator (RR). The interaction between an IP and its sensor, which is highly specific, leads to activation of the cognate RR which in turn binds to regulated promoters and activates gene expression. The HPKs and RRs are built up by conserved modules, and the signalling between them within a network is efficient and directional, and can easily be activated by exogenously added synthetic IPs. Consequently, components from such regulatory networks have successfully been exploited in construction of a number of inducible gene expression systems. In this review, we discuss some well-characterised quorum sensing networks involved in bacteriocin production in lactobacilli, with special focus on the use of the regulatory components in gene expression and on lactobacilli as potential delivery vehicle for therapeutic and vaccine purposes.

Heterologous protein secretion by Lactobacillus plantarum using homologous signal peptides

AIMS

To test seven selected putative signal peptides from Lactobacillus plantarum WCFS1 in terms of their ability to drive secretion of two model proteins in Lact. plantarum, and to compare the functionality of these signal peptides with that of well-known heterologous signal peptides (Usp45, M6).

METHODS AND RESULTS

Signal peptide functionality was assessed using a series of modular derivatives of the pSIP vectors for peptide pheromone-controlled high-level gene expression in lactobacilli. Several of the constructs with homologous signal peptides yielded similar or higher reporter protein activities than constructs with heterologous signal peptides. Two of the homologous signal peptides (Lp_0373 and Lp_0600) appeared as especially promising candidates for directing secretion, as they were among the best performing with both reporter proteins.

CONCLUSIONS

We have identified homologous signal peptides for high-level secretion of heterologous proteins in Lact. plantarum. With the model proteins, some of these performed better than commonly used heterologous signal peptides.

SIGNIFICANCE AND IMPACT OF THE STUDY

The homologous signal peptides tested out, in this study, could be useful in food-grade systems for secretion of interesting proteins in Lact. plantarum. The constructed modular secretion vectors are easily accessible for rapid signal peptide screening.

The tomato pathogen Clavibacter michiganensis ssp. michiganensis: producer of several antimicrobial substances

AIM

To purify and analyse antimicrobial substances produced by the tomato pathogen Clavibacter michiganensis ssp. michiganensis (Cmm), with potential application in control of Clavibacter michiganensis ssp. sepedonicus (Cms), the causal agent of bacterial ring rot of potato.

METHODS AND RESULTS

After selection of a suitable producer and indicator strain, antimicrobial compounds were isolated using chromatographic techniques. The resulting preparations were analysed with respect to heat and protease sensitivity, amino acid composition, amino acid sequence and mass. Using this procedure we discovered one post-translationally modified 2145 Da peptide bacteriocin, one 14 kDa antimicrobial protein as well as low molecular weight (<1000 Da) antimicrobial compounds, putatively belonging to the tunicamycin family.

CONCLUSIONS

Clavibacter michiganensis ssp. michiganensis produces various antibacterial substances that are active against Cms.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study describes the first attempt to characterize antimicrobial substances from Cmm at the molecular level. This is an important step towards investigation of the possible use of these compounds to control the potato ring rot pathogen.

Purification, characterization, and gene sequence of michiganin A, an actagardine-like lantibiotic produced by the tomato pathogen Clavibacter michiganensis subsp. michiganensis

Members of the actinomycete genus Clavibacter are known to produce antimicrobial compounds, but so far none of these compounds has been purified and characterized. We have isolated an antimicrobial peptide, michiganin A, from the tomato pathogen Clavibacter michiganensis subsp. michiganensis, using ammonium sulfate precipitation followed by cation-exchange and reversed-phase chromatography steps. Upon chemical derivatization of putative dehydrated amino acids and lanthionine bridges by alkaline ethanethiol, Edman degradation yielded sequence information that proved to be sufficient for cloning of the gene by a genome-walking strategy. The mature unmodified peptide consists of 21 amino acids, SSSGWLCTLTIECGTIICACR. All of the threonine residues undergo dehydration, and three of them interact with cysteines via thioether bonds to form methyllanthionine bridges. Michiganin A resembles actagardine, a type B lantibiotic with a known three-dimensional structure, produced by Actinoplanes liguriae, which is a filamentous actinomycete. The DNA sequence of the gene showed that the michiganin A precursor contains an unusual putative signal peptide with no similarity to well-known secretion signals and only very limited similarity to the (only two) available leader peptides of other type B lantibiotics. Michiganin A inhibits the growth of Clavibacter michiganensis subsp. sepedonicus, the causal agent of ring rot of potatoes, with MICs in the low nanomolar range. Thus, michiganin A may have some potential in biological control of potato ring rot.

Synthesis and evaluation of a 99mTechnetium labeled chitin-binding protein as potential specific radioligand for the detection of fungal infections in mice

AIM

Radiopharmaceuticals can be used to exploit differences between microorganisms in order to distinguish fungal from bacterial infection. Chitin, abundant in the cell wall of fungi, is not present in mammalian or bacterial cells and therefore represents a highly specific target to localize fungal infection. In this study, we have examined the potential of chitin-binding protein (CBP21) from Serratia marcescens as a specific radiotracer for the detection of invasive fungal infections.

METHODS

CBP21 was labeled with 99mTc via hydrazinonicotinamide (HYNIC) and its characteristics were analyzed. In vitro binding studies with polymorphic chitin forms and microorganisms (fungi as well as bacteria) were performed. In vivo biodistribution of the compound was studied in immunocompromised mice with bacterial and fungal infections in the left and right thigh muscle, respectively, using 99mTc-HYNIC-myoglobin as size-matched control and 67Ga-citrate as positive control. Scintigraphic images were acquired at 1 and 7 h postinjection of the tracer.

RESULTS

99mTc-HYNIC-CBP21 was labeled with a radiochemical yield of 61% and a specific activity of 22.3 MBq/nmol. Highest in vitro binding percentages were found with beta-chitin (86.8+/-2.4%). Binding interactions to fungi were higher than to bacteria (P<0.05). In vivo, best ratios of fungal infection versus bacterial infection were seen at 5 and 7 h (3.6+/-1.2 and 2.9+/-1.4, respectively) postinjection of the tracer. Maximum uptake of the tracer in fungal infections (0.63+/-0.11%ID/g) at 7 h was significantly (P<0.05) higher than uptake seen in bacterial infections (0.34+/-0.11%ID/g) or the uptake of 99mTc-HYNIC-myoglobin (P<0.05) in the same infections (0.35+/-0.11%ID/g, respectively, 0.3+/-0.01%ID/g).

CONCLUSIONS

This study shows that 99mTc-HYNIC-CBP21 is able to specifically interact with chitin in vitro. Scintigraphy and postmortem in vivo data indicate that 99mTc-HYNIC-CBP21 is able to distinguish fungal infection from bacterial infection probably due to a specific interaction of the protein with the chitin in the fungal cell wall.

Growth of Lactobacillus plantarum in media containing hydrolysates of fish viscera

AIMS

To compare growth of Lactobacillus plantarum on media containing hydrolysates (peptones) from cod viscera with growth on commercial media.

METHODS AND RESULTS

Growth of Lact. plantarum on various fish peptones and commercial peptones/extracts was evaluated using both a Bioscreen apparatus (microtiter plates, no pH control) and fermentors (with pH control). Generally, the performance of the fish peptones was good and only beaten by the performance of yeast extract. Replacement of the 22 g l(-1) complex nitrogen source in standard MRS medium with only 5 g l(-1) fish peptone reduced the biomass yield with only 10%, whereas replacement with a mixture of 2.5 g l(-1) fish peptone and 2.5 g l(-1) yeast extract increased the biomass yield by 10%.

CONCLUSIONS

Peptones derived from cod viscera support excellent growth of Lact. plantarum.

SIGNIFICANCE AND IMPACT OF THE STUDY

We show that peptones derived from cod viscera are promising constituents of growth media for fastidious food bacteria such as lactobacilli. Media containing these peptones show excellent performance while problems associated with the use of meat-derived peptones (BSE, kosher status) or plant-derived peptones (genetically modified organisms) are avoided.

High-level gene expression in Lactobacillus plantarum using a pheromone-regulated bacteriocin promoter

AIMS

To use promoters and regulatory genes involved in the production of the bacteriocin sakacin P to obtain high-level regulated gene expression in Lactobacillus plantarum.

METHODS AND RESULTS

In a plasmid containing all three operons naturally involved in sakacin P production, the genes encoding sakacin P and its immunity protein were replaced by the aminopeptidase N gene from Lactococcus lactis (pepN) or the beta-glucuronidase gene from Escherichia coli (gusA). The new genes were precisely fused to the start codon of the sakacin P gene and the stop codon of the immunity gene. This set-up permitted regulated (external pheromone controlled) overexpression of both reporter genes in L. plantarum NC8. For PepN, production levels amounted to as much as 40% of total cellular protein.

CONCLUSIONS

Promoters and regulatory genes involved in production of sakacin P are suitable for establishing inducible high-level gene expression in L. plantarum.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study describes a system for controllable gene expression in lactobacilli, giving some of the highest expression levels reported so far in this genus.

Use of bacteriocin promoters for gene expression in Lactobacillus plantarum C11

AIMS

To exploit promoters involved in production of the bacteriocin sakacin P for regulated overexpression of genes in Lactobacillus plantarum C11.

METHODS AND RESULTS

Production of sakacin P by Lact. sakei LTH673 is controlled by a peptide-based quorum sensing system that drives strong, regulated promoters. One of these promoters (PorfX) was used to establish regulated overexpression of genes encoding chloramphenicol acetyltransferase from Bacillus pumilus, aminopeptidase N from Lactococcus lactis or chitinase B from Serratia marcescens in Lact. plantarum C11, a strain that naturally possesses the regulatory machinery that is necessary for promoter activation. The expression levels obtained were highly dependent on which gene was used and on how the promoter was coupled to this gene. The highest expression levels (14% of total cellular protein) were obtained with the aminopeptidase N gene translationally fused to the regulated promoter.

CONCLUSIONS

Sakacin promoters permit regulated expression of a variety of genes in Lact. plantarum C11.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows the usefulness of regulated bacteriocin promoters for developing new gene expression systems for lactic acid bacteria, in particular lactobacilli.

Psammaplin A, a chitinase inhibitor isolated from the Fijian marine sponge Aplysinella rhax

Several brominated tyrosine derived compounds, psammaplins A (1), K (2) and L (3) as well as bisaprasin (4) were isolated from the Fijian marine sponge Aplysinella rhax during a bioassay guided isolation protocol. Their structures were determined using NMR and MS techniques. Psammaplin A was found to moderately inhibit chitinase B from Serratia marcescens, the mode of inhibition being non-competitive. Crystallographic studies suggest that a disordered psammaplin A molecule is bound near the active site. Interestingly, psammaplin A was found to be a potent antifungal agent.

Structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 A resolution

The crystal structure of the inactive D140N mutant of Serratia marcescens was refined to 1.45 A resolution. The structure of the mutant was essentially identical to that of the wild type, with the exception of a rotation of Asp142 in the catalytic centre. In the mutant, this residue interacts with the catalytic acid (Glu144) and not with residue 140 as in the wild type. Thus, the 500-fold decrease in activity in the D140N mutant seems to be largely mediated by an effect on Asp142, confirming the crucial role of the latter residue in catalysis.