Perspectives for the application of Ustilaginaceae as biotech cell factories

2021 ◽  
Author(s):  
Nick Wierckx ◽  
Katharina Miebach ◽  
Nina Ihling ◽  
Kai P. Hussnaetter ◽  
Jochen Büchs ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Process Development ◽  
Model Organism ◽  
Value Added ◽  
Detailed Knowledge ◽  
Product Specificity ◽  
Cell Factories ◽  
Hydrolytic Activities ◽  
The Family ◽  
Fundamental Research

Abstract Basidiomycetes fungi of the family Ustilaginaceae are mainly known as plant pathogens causing smut disease on crops and grasses. However, they are also natural producers of value-added substances like glycolipids, organic acids, polyols, and harbor secretory enzymes with promising hydrolytic activities. These attributes recently evoked increasing interest in their biotechnological exploitation. The corn smut fungus Ustilago maydis is the best characterized member of the Ustilaginaceae. After decades of research in the fields of genetics and plant pathology, a broad method portfolio and detailed knowledge on its biology and biochemistry are available. As a consequence, U. maydis has developed into a versatile model organism not only for fundamental research but also for applied biotechnology. Novel genetic, synthetic biology, and process development approaches have been implemented to engineer yields and product specificity as well as for the expansion of the repertoire of produced substances. Furthermore, research on U. maydis also substantially promoted the interest in other members of the Ustilaginaceae, for which the available tools can be adapted. Here, we review the latest developments in applied research on Ustilaginaceae towards their establishment as future biotech cell factories.

scholarly journals Functional Characterization of a 28-Kilobase Catabolic Island from Pseudomonas sp. Strain M1 Involved in Biotransformation of β-Myrcene and Related Plant-Derived Volatiles

2017 ◽  
Vol 83 (9) ◽  
Author(s):  
Pedro Soares-Castro ◽  
Pedro Montenegro-Silva ◽  
Hermann J. Heipieper ◽  
Pedro M. Santos
Keyword(s):  
Metabolic Engineering ◽  
Functional Characterization ◽  
Regulatory Protein ◽  
Model Organism ◽  
Detailed Knowledge ◽  
Initial Oxidation ◽  
Content Type ◽  
Cell Factories ◽  
Analytical Approaches

ABSTRACT Pseudomonas sp. strain M1 is able to mineralize highly hydrophobic and recalcitrant compounds, such as benzene, phenol, and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such a spectrum of compounds as the sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of strain M1 regarding β-myrcene catabolism was elucidated in this work, with a focus on the biocatalytical potential of the β-myrcene-associated core code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units. Functional characterization of this locus with promoter probes and analytical approaches validated the genetic organization predicted in silico and associated the β-myrcene-induced promoter activity to the production of β-myrcene derivatives. Notably, by using a whole-genome mutagenesis strategy, different genotypes of the 28-kb GI were generated, resulting in the identification of a novel putative β-myrcene hydroxylase, responsible for the initial oxidation of β-myrcene into myrcen-8-ol, and a sensor-like regulatory protein, whose inactivation abolished the myr + trait of M1 cells. Moreover, it was demonstrated that the range of monoterpene substrates of the M1 enzymatic repertoire, besides β-myrcene, also includes other acyclic (e.g., β-linalool) and cyclic [e.g., R-(+)-limonene and (−)-β-pinene] molecules. Our findings are the cornerstone for following metabolic engineering approaches and hint at a major role of the 28-kb GI in the biotransformation of a broad monoterpene backbone spectrum for its future biotechnological applications. IMPORTANCE Information regarding microbial systems able to biotransform monoterpenes, especially β-myrcene, is limited and focused mainly on nonsystematic metabolite identification. Complete and detailed knowledge at the genetic, protein, metabolite, and regulatory levels is essential in order to set a model organism or a catabolic system as a biotechnology tool. Moreover, molecular characterization of reported systems is scarce, almost nonexistent, limiting advances in the development of optimized cell factories with strategies based on the new generation of metabolic engineering platforms. This study provides new insights into the intricate molecular functionalities associated with β-myrcene catabolism in Pseudomonas, envisaging the production of a molecular knowledge base about the underlying catalytic and regulatory mechanisms of plant-derived volatile catabolic pathways.

An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)

Zootaxa ◽  
2018 ◽  
Vol 4415 (1) ◽  
pp. 45 ◽  
Author(s):  
PIOTR GĄSIOREK ◽  
DANIEL STEC ◽  
WITOLD MOREK ◽  
ŁUKASZ MICHALCZYK
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Model Organism ◽  
Laboratory Strain ◽  
Sensu Stricto ◽  
Nominal Species ◽  
28S Rrna ◽  
The Family ◽  
The 19Th Century ◽  
Hypsibius Dujardini

A laboratory strain identified as “Hypsibius dujardini” is one of the best studied tardigrade strains: it is widely used as a model organism in a variety of research projects, ranging from developmental and evolutionary biology through physiology and anatomy to astrobiology. Hypsibius dujardini, originally described from the Île-de-France by Doyère in the first half of the 19th century, is now the nominal species for the superfamily Hypsibioidea. The species was traditionally considered cosmopolitan despite the fact that insufficient, old and sometimes contradictory descriptions and records prevented adequate delineations of similar Hypsibius species. As a consequence, H. dujardini appeared to occur globally, from Norway to Samoa. In this paper, we provide the first integrated taxonomic redescription of H. dujardini. In addition to classic imaging by light microscopy and a comprehensive morphometric dataset, we present scanning electron photomicrographs, and DNA sequences for three nuclear markers (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial marker (COI) that are characterised by various mutation rates. The results of our study reveal that a commercially available strain that is maintained in many laboratories throughout the world, and assumed to represent H. dujardini sensu stricto, represents, in fact, a new species: H. exemplaris sp. nov. Redescribing the nominal taxon for Hypsibiidae, we also redefine the family and amend the definitions of the subfamily Hypsibiinae and the genus Hypsibius. Moreover, we transfer H. arcticus (Murray, 1907) and Hypsibius conifer Mihelčič, 1938 to the genus Ramazzottius since the species exhibit claws and eggs of the Ramazzottius type. Finally, we designate H. fuhrmanni as subjectively invalid because the extremely poor description precludes identifying neotype material. 

scholarly journals Development of New Product/Process Development Procedure for SMEs

Organizacija ◽  
2010 ◽  
Vol 43 (2) ◽  
pp. 76-86 ◽  
Author(s):  
Mateja Šenk ◽  
Peter Metlikovič ◽  
Matjaž Maletič ◽  
Boštjan Gomišček
Keyword(s):  
Automotive Industry ◽  
Process Development ◽  
Cost Management ◽  
Value Added ◽  
New Product ◽  
Quality Planning ◽  
Design For Six Sigma ◽  
Plastic Processing ◽  
New Process ◽  
Development Procedure

Development of New Product/Process Development Procedure for SMEsThe result of our research is a developed and implemented set of activities for new process or product development (NPD procedure) for SMEs environment in the plastic processing industry, which enables the production of products and services with a high value added.The developed NPD procedure consists of five consecutive and overlapping steps: attracting orders, designing a project, developing a product, developing a process and zero production series. Each distinct step is further divided into sub-activities supported by adequate methods and managed in an information system. Investigated and included were three different methodologies use for NPD procedure in the automotive industry such as Advanced Product Quality Planning (APQP), Design for Six Sigma (DFSS) and Stage/Gate methodology.The results presented in the paper show that the developed NPD procedure significantly improved NPD in terms of cost management and time-effectiveness.

Value-added bioplastics from services of wastewater treatment

2015 ◽  
Vol 10 (3) ◽  
pp. 546-555 ◽  
Author(s):  
M. Arcos-Hernández ◽  
L. Montaño-Herrera ◽  
O. Murugan Janarthanan ◽  
L. Quadri ◽  
S. Anterrieu ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Real Life ◽  
Value Added ◽  
Renewable Resource ◽  
Economic Networks ◽  
Technical Feasibility ◽  
Material Supply ◽  
The Social ◽  
Essential Services ◽  
Fundamental Research

Pilot and prototyping scale investigations were undertaken in order to evaluate the technical feasibility of producing value-added biopolymers (polyhydroxyalkanoates (PHAs)) as a by-product to essential services of wastewater treatment and environmental protection. A commonly asked question concerns PHA quality that may be expected from surplus biomass produced during biological treatment for water quality improvement. This paper summarizes the findings from a collection of investigations. Alongside the summarized technical efforts, attention has been paid to the social and economic networks. Such networks are needed in order to nurture circular economies that would drive value chains in renewable resource processing from contaminated water amelioration into renewable value-added bioplastic products and services. We find commercial promise in the polymer quality and in the process technical feasibility. The next challenge ahead does not reside so much any more in fundamental research and development of the technology but, rather, in social-economic steps that will be necessary to realize first demonstration scale polymer production activities. It is a material supply that will stimulate niche business opportunities that can grow and stimulate technology pull with benefit of real life material product market combinations.

Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

Fermentation ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. 220
Author(s):  
Wubliker Dessie ◽  
Zongcheng Wang ◽  
Xiaofang Luo ◽  
Meifeng Wang ◽  
Zuodong Qin
Keyword(s):  
Succinic Acid ◽  
In Silico ◽  
Value Added ◽  
Research Progress ◽  
Efficient Production ◽  
Actinobacillus Succinogenes ◽  
Cell Factories ◽  
In Silico Studies ◽  
Current Scenario ◽  
Critical Problems

Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.

scholarly journals Computational Analysis of Dynamic Light Exposure of Unicellular Algal Cells in a Flat-Panel Photobioreactor to Support Light-Induced CO2 Bioprocess Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Nicolò S. Vasile ◽  
Alessandro Cordara ◽  
Giulia Usai ◽  
Angela Re
Keyword(s):  
Light Transmission ◽  
Light Exposure ◽  
Model Organism ◽  
Cell Factory ◽  
Bioprocess Development ◽  
Cultivation Conditions ◽  
Flat Panel ◽  
Modeling Framework ◽  
Cell Factories ◽  
Cell Trajectories

Cyanobacterial cell factories trace a vibrant pathway to climate change neutrality and sustainable development owing to their ability to turn carbon dioxide-rich waste into a broad portfolio of renewable compounds, which are deemed valuable in green chemistry cross-sectorial applications. Cell factory design requires to define the optimal operational and cultivation conditions. The paramount parameter in biomass cultivation in photobioreactors is the light intensity since it impacts cellular physiology and productivity. Our modeling framework provides a basis for the predictive control of light-limited, light-saturated, and light-inhibited growth of the Synechocystis sp. PCC 6803 model organism in a flat-panel photobioreactor. The model here presented couples computational fluid dynamics, light transmission, kinetic modeling, and the reconstruction of single cell trajectories in differently irradiated areas of the photobioreactor to relate key physiological parameters to the multi-faceted processes occurring in the cultivation environment. Furthermore, our analysis highlights the need for properly constraining the model with decisive qualitative and quantitative data related to light calibration and light measurements both at the inlet and outlet of the photobioreactor in order to boost the accuracy and extrapolation capabilities of the model.

Metabolic engineering of glycosylated polyketide biosynthesis

2018 ◽  
Vol 2 (3) ◽  
pp. 389-403 ◽  
Author(s):  
Ramesh Prasad Pandey ◽  
Prakash Parajuli ◽  
Jae Kyung Sohng
Keyword(s):  
Natural Products ◽  
Metabolic Engineering ◽  
Value Added ◽  
Chemical Diversity ◽  
Yeast Cells ◽  
Microbial Cell Factories ◽  
Cell Factories ◽  
Modification Method ◽  
Post Modification ◽  
Microbial Biosynthesis

Microbial cell factories are extensively used for the biosynthesis of value-added chemicals, biopharmaceuticals, and biofuels. Microbial biosynthesis is also realistic for the production of heterologous molecules including complex natural products of plant and microbial origin. Glycosylation is a well-known post-modification method to engineer sugar-functionalized natural products. It is of particular interest to chemical biologists to increase chemical diversity of molecules. Employing the state-of-the-art systems and synthetic biology tools, a range of small to complex glycosylated natural products have been produced from microbes using a simple and sustainable fermentation approach. In this context, this review covers recent notable metabolic engineering approaches used for the biosynthesis of glycosylated plant and microbial polyketides in different microorganisms. This review article is broadly divided into two major parts. The first part is focused on the biosynthesis of glycosylated plant polyketides in prokaryotes and yeast cells, while the second part is focused on the generation of glycosylated microbial polyketides in actinomycetes.

scholarly journals Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta)

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 404 ◽  
Author(s):  
Alexandria Creasy ◽  
Karyna Rosario ◽  
Brittany Leigh ◽  
Larry Dishaw ◽  
Mya Breitbart
Keyword(s):  
Marine Invertebrate ◽  
Animal Health ◽  
Relative Proportion ◽  
Model Organism ◽  
Model System ◽  
Microbial Interactions ◽  
Phylogenetic Groups ◽  
Surrounding Water ◽  
The Family ◽  
Dsdna Viruses

Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.

Functional Properties of Plasmids as Related to Enumeration of Bacteria Important to the Food Microbiologist

1978 ◽  
Vol 41 (1) ◽  
pp. 44-47 ◽  
Author(s):  
CLIFFORD HOWELL ◽  
WILLIAM J. MARTIN
Keyword(s):  
Bacterial Species ◽  
Animal Husbandry ◽  
Selective Advantage ◽  
Detailed Knowledge ◽  
Biochemical Tests ◽  
Pathogenic Potential ◽  
Bacterial Populations ◽  
Phenotypic Characters ◽  
Resistance To Antibiotics ◽  
The Family

Plasmids are extrachromosomal elements that behave like auxiliary chromosomes and contain the basic structure of the replicating unit. They were initially recognized by the unusual phenotypic characteristics they confer upon a cell, such as ability to promote genetic transfer by conjugation; resistance to antibiotics and metal ions; production of bacteriocins, toxins, antigens; and other factors. Much of the work on plasmids and plasmid-mediated characteristics has been conducted with various genera and species of the family Enterobacteriaceae. Present data indicate that although plasmid transfer occurs with variable frequency, intergeneric transfer within the family is invariably successful. Although a great deal of investigation has been focused on plasmid-mediated resistance to antibiotics, many workers have determined that a number of plasmids control other phenotypic characters. For example such plasmids appear to mediate production of bacterial products and/or enzymes which may confer a selective ecological advantage to bacteria in their inter-relationships with their hosts and other microorganisms. The isolation of these phenotypically altered microorganisms by food, medical, and public health microbiologists may signify an important ubiquitous phenomenon. There is increasing evidence that selective forces operate in both the laboratory and in nature which should alert the microbiologist that any of the present-day identification schema must be utilized with some caution. To this end technical advances in identification of microorganisms by use of a large battery of biochemical tests has increased the accuracy of identification and measurably reduced the misidentification of atypical bacteria. Availability of such data may assist the microbiologist to establish baseline information essential for development of prospective studies for defining the reservoirs of phenotypically altered microorganisms and their pathogenic potential for the general population. The full importance of plasmid-mediated characteristics in bacterial populations in food products and the role they will play in the future is largely unknown. The origin and selective advantage that strains harboring plasmids in the natural ecology is also unknown. Detailed knowledge of microorganisms maintaining plasmids may be important economically, since the emergence of a number of antibiotic-resistant microorganisms may have contributed a significant role in development of disease among domestic animals because oft he manner in which animal husbandry is practiced in many countries. Extrapolated, one could speculate about an ever-increasing reservoir of similar bacterial species, potentially transmissible to man. Because the factors which control mobilization of plasmids and the important ecological selective advantage conferred upon bacterial populations by plasmids, it is essential that we as microbiologists become cognizant of their existence and to fully understand the mechanisms of perpetuation of plasmid-mediated characteristics.

scholarly journals SaxA-Mediated Isothiocyanate Metabolism in Phytopathogenic Pectobacteria

2016 ◽  
Vol 82 (8) ◽  
pp. 2372-2379 ◽  
Author(s):  
Cornelia U. Welte ◽  
Jamila F. Rosengarten ◽  
Rob M. de Graaf ◽  
Mike S. M. Jetten
Keyword(s):  
Defense Mechanisms ◽  
Plant Pathogens ◽  
Carbonyl Sulfide ◽  
Food Preservation ◽  
Beta Lactam ◽  
Content Type ◽  
Beta Lactam Antibiotics ◽  
The Family ◽  
Class B ◽  
Phenylethyl Isothiocyanate

ABSTRACTPectobacteria are devastating plant pathogens that infect a large variety of crops, including members of the family Brassicaceae. To infect cabbage crops, these plant pathogens need to overcome the plant's antibacterial defense mechanisms, where isothiocyanates are liberated by hydrolysis of glucosinolates. Here, we found that aPectobacteriumisolate from the gut of cabbage root fly larvae was particularly resistant to isothiocyanate and even seemed to benefit from the abundantBrassicaroot metabolite 2-phenylethyl isothiocyanate as a nitrogen source in an ecosystem where nitrogen is scarce. ThePectobacteriumisolate harbored a naturally occurring mobile plasmid that contained asaxoperon. We hypothesized that SaxA was the enzyme responsible for the breakdown of 2-phenylethyl isothiocyanate. Subsequently, we heterologously produced and purified the SaxA protein and characterized the recombinant enzyme. It hydrolyzed 2-phenylethyl isothiocyanate to yield the products carbonyl sulfide and phenylethylamine. It was also active toward another aromatic isothiocyanate but hardly toward aliphatic isothiocyanates. It belongs to the class B metal-dependent beta-lactamase fold protein family but was not, however, able to hydrolyze beta-lactam antibiotics. We discovered that several copies of thesaxAgene are widespread in full and draftPectobacteriumgenomes and therefore hypothesize that SaxA might be a new pathogenicity factor of the genusPectobacterium, possibly compromising food preservation strategies using isothiocyanates.

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