scholarly journals Shotgun proteomics reveals putative polyesterases in the secretome of the rock-inhabiting fungus Knufia chersonesos

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Donatella Tesei ◽  
Felice Quartinello ◽  
Georg M. Guebitz ◽  
Doris Ribitsch ◽  
Katharina Nöbauer ◽  
...  

Abstract Knufia chersonesos is an ascomycotal representative of black fungi, a morphological group of polyextremotolerant melanotic fungi, whose ability to resort to recalcitrant carbon sources makes it an interesting candidate for degradation purposes. A secretome screening towards polyesterases was carried out for the fungus and its non-melanized mutant, grown in presence of the synthetic copolyester Polybutylene adipate terephthalate (PBAT) as additional or sole carbon source, and resulted in the identification of 37 esterolytic and lipolytic enzymes across the established cultivation conditions. Quantitative proteomics allowed to unveil 9 proteins being constitutively expressed at all conditions and 7 which were instead detected as up-regulated by PBAT exposure. Protein functional analysis and structure prediction indicated similarity of these enzymes to microbial polyesterases of known biotechnological use such as MHETase from Ideonella sakaiensis and CalA from Candida antarctica. For both strains, PBAT hydrolysis was recorded at all cultivation conditions and primarily the corresponding monomers were released, which suggests degradation to the polymer’s smallest building block. The work presented here aims to demonstrate how investigations of the secretome can provide new insights into the eco-physiology of polymer degrading fungi and ultimately aid the identification of novel enzymes with potential application in polymer processing, recycling and degradation.

2019 ◽  
Author(s):  
Mitchell G. Thompson ◽  
Luis E. Valencia ◽  
Jacquelyn M. Blake-Hedges ◽  
Pablo Cruz-Morales ◽  
Alexandria E. Velasquez ◽  
...  

ABSTRACTPseudomonas putida is a promising bacterial chassis for metabolic engineering given its ability to metabolize a wide array of carbon sources, especially aromatic compounds derived from lignin. However, this omnivorous metabolism can also be a hindrance when it can naturally metabolize products produced from engineered pathways. Herein we show that P. putida is able to use valerolactam as a sole carbon source, as well as degrade caprolactam. Lactams represent important nylon precursors, and are produced in quantities exceeding one million tons per year[1]. To better understand this metabolism we use a combination of Random Barcode Transposon Sequencing (RB-TnSeq) and shotgun proteomics to identify the oplBA locus as the likely responsible amide hydrolase that initiates valerolactam catabolism. Deletion of the oplBA genes prevented P. putida from growing on valerolactam, prevented the degradation of valerolactam in rich media, and dramatically reduced caprolactam degradation under the same conditions. Deletion of oplBA, as well as pathways that compete for precursors L-lysine or 5-aminovalerate, increased the titer of valerolactam from undetectable after 48 hours of production to ~90 mg/L. This work may serve as a template to rapidly eliminate undesirable metabolism in non-model hosts in future metabolic engineering efforts.


2012 ◽  
Author(s):  
Mohd. Sahaid Hj. Kalil ◽  
Muhammad Zaki ◽  
Wan Mohtar Wan Yusoff ◽  
Mohammad Ramlan Mohd. Salleh

Penyelidikan ini bertujuan untuk menyaring substrat organik bagi untuk penghasilan sel–sel A. woodii teraruh demetilase. Pertumbuhan A. woodii dilakukan dalam medium “Balch” yang mengandungi sumber karbon berbeza dalam keadaan anaerobik. Sebanyak sebelas substrat telah diuji iaitu anisol, 2– dan 3–metoksifenol, asid vanilik, asid siringik, asid 2,3,4–, 2,4,5– dan 3,4,5–trimetoksi benzoik, 2,3,4–, 2,4,5– dan 3,4,5–trimetoksi benzil alkohol. 2–metoksifenol merupakan substrat terbaik untuk pertumbuhan A. woodii pada kadar pertumbuhan spesifik 0.14 j–1. Penghasilan sel–sel teraruh demetilase dilakukan dalam kultur kemostat pada kadar pencairan (D) 0.0j–1. Sel-sel pada keadaan mantap dituai dalam keadaan anaerobik dan dipekatkan sebelum digunakan. Pertumbuhan A. woodii didapati maksimum dengan menggunakan kepekatan 0.62 g/L 2–metoksifenol sebagai sumber karbon tunggal. Tindak balas penyahmetilan oleh sel–sel A. woodii meningkat sebanyak 78% apabila 2–metoksifenol sebanyak 0.31 g/L ditambah dalam medium yang mengandungi fruktosa (1% w/v) semasa kultur kemostat. Kata kunci: tindak balas penyahmetilan; demetilase; sel-sel tertuai; metosiaromatik, Acetobacteriumwoodii The objective of this project was to screen organic substrate suitable for the growth of A. woodii, and as for the production of demethylase. A. woodii was grown in “Balch” medium containing different carbon sources. Eleven substrates were tested including anisole, 2– and 3–methoxyphenol, vanilic acid, syringic acid, 2,3,4–, 2,4,5– and 3,4,5–trimethoxy benzoic acid and 2,3,4–, 2,4,5– and 3,4,5–trimethoxy benzyl alcohol. It was found that 2–methoxyphenol was the best substrate with a specific growth rate of 0.14 h–1. The production of demethylase induced cells was carried out in a chemostat culture at a dilution rate (D) of 0.08 h–1. Cells were harvested at steady state of growth and concentrated before use. Optimal concentration of 2–methoxvphenol as the sole carbon source was 0.62 g/L. Demethylation reaction of 0.31 g/L 2–methoxyphenol by induced culture increases 78% relative to the chemostat culture containing only fructose. Key words: Demethylation reaction; demethylase; harvested cells; methoxyaromatic; Acetobacteriumwoodii


2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Arief Izzairy Zamani ◽  
Susann Barig ◽  
Sarah Ibrahim ◽  
Hirzun Mohd. Yusof ◽  
Julia Ibrahim ◽  
...  

Abstract Background Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lacking. Selected fungi that can grow in acidic mineral salt media (MSM) with vegetable oil had been identified recently. Hence, this study aimed to investigate the overall metabolite changes of an omnipotent fungus and to reveal changes at central carbon metabolism corresponding to both carbon sources. Results Targeted and non-targeted metabolomics for both polar and semi-polar metabolites of Phialemonium curvatum AWO2 (DSM 23903) cultivated in MSM with palm oil (MSM-P) or glucose (MSM-G) as carbon sources were obtained. Targeted metabolomics on central carbon metabolism of tricarboxylic acid (TCA) cycle and glyoxylate cycle were analysed using LC–MS/MS-TripleQ and GC–MS, while untargeted metabolite profiling was performed using LC–MS/MS-QTOF followed by multivariate analysis. Targeted metabolomics analysis showed that glyoxylate pathway and TCA cycle were recruited at central carbon metabolism for triglyceride and glucose catabolism, respectively. Significant differences in organic acids concentration of about 4- to 8-fold were observed for citric acid, succinic acid, malic acid, and oxaloacetic acid. Correlation of organic acids concentration and key enzymes involved in the central carbon metabolism was further determined by enzymatic assays. On the other hand, the untargeted profiling revealed seven metabolites undergoing significant changes between MSM-P and MSM-G cultures. Conclusions Overall, this study has provided insights on the understanding on the effect of triglycerides and sugar as carbon source in fungi global metabolic pathway, which might become important for future optimization of carbon flux engineering in fungi to improve organic acids production when vegetable oil is applied as the sole carbon source.


1999 ◽  
Vol 181 (18) ◽  
pp. 5600-5605 ◽  
Author(s):  
Jan W. Vrijbloed ◽  
Katja Zerbe-Burkhardt ◽  
Ananda Ratnatilleke ◽  
Andreas Grubelnik-Leiser ◽  
John A. Robinson

ABSTRACT The coenzyme B12-dependent isobutyryl coenzyme A (CoA) mutase (ICM) and methylmalonyl-CoA mutase (MCM) catalyze the isomerization of n-butyryl-CoA to isobutyryl-CoA and of methylmalonyl-CoA to succinyl-CoA, respectively. The influence that both mutases have on the conversion of n- and isobutyryl-CoA to methylmalonyl-CoA and the use of the latter in polyketide biosynthesis have been investigated with the polyether antibiotic (monensin) producer Streptomyces cinnamonensis. Mutants prepared by inserting a hygromycin resistance gene (hygB) into either icmA or mutB, encoding the large subunits of ICM and MCM, respectively, have been characterized. The icmA::hygB mutant was unable to grow on valine or isobutyrate as the sole carbon source but grew normally on butyrate, indicating a key role for ICM in valine and isobutyrate metabolism in minimal medium. ThemutB::hygB mutant was unable to grow on propionate and grew only weakly on butyrate and isobutyrate as sole carbon sources. 13C-labeling experiments show that in both mutants butyrate and acetoacetate may be incorporated into the propionate units in monensin A without cleavage to acetate units. Hence, n-butyryl-CoA may be converted into methylmalonyl-CoA through a carbon skeleton rearrangement for which neither ICM nor MCM alone is essential.


Author(s):  
Olga I. Kiselyova ◽  
◽  
Sergey V. Lutsenko ◽  
Natalia B. Feldman ◽  
Irina A. Gavryushina ◽  
...  

Bacterial cellulose (BC) is a natural polymer that has a number of unique properties that determine the need to synthesize large amounts of it and to search the ways to increase the productivity of strains and to optimize the nutritive media. It is known that the choice of the producer for BC synthesis has an impact on its final properties and on the productivity of this polymer production. Under static liquid phase cultivation conditions, all cellulose-producing bacteria form a uniform film on the medium surface that serves as a scaffold for cells immobilization, thus providing them with the access to the air/liquid interface, where the access to oxygen is not limited. Meanwhile, when cultivation goes under agitating conditions, most of Gluconacetobacter xylinus strains produce less cellulose in form of globules of various sizes, despite the better oxygen access. Several authors explain the lower cellulose outcome when cultivated under agitated conditions by the appearance of spontaneous mutants that do not produce cellulose in the population. It was revealed that when grown on agarized media, cellulosenon- producing mutants form colonies of a specific mucoid type, while non-mucoid phenotype cells form smooth colonies of non-mucoid type. To our knowledge, there is no published research on the impact of cultivation conditions and nutritive medium composition on the appearance of spontaneous phenotype mutations in the population of Gluconacetobacter hansenii representatives. The aim of the present research is to elucidate the impact of the carbon source on the productivity of G. hansenii strain and the appearance of cellulose-negative mutants under static cultivation conditions. We studied the strain G. hansenii GH 1/2008 (VKPM В-10547) as a BC source. Liquid phase static cultivation of G. hansenii GH 1/2008 was carried out using the modified Hestrin-Schramm (HS) medium, containing 4% of monosaccharides (glucose, fructose and galactose) or disaccharides (sucrose, maltose, lactose) as carbon sources. The occurrence of mutants was calculated considering phenotypes of colonies obtained by seeding the samples of cultural liquid and wash-offs of cells from films produced by the cultivation of the producer on modified agarized HS media. The polymer outcome was expressed as the film absolute dry weight (a.d.w.) per cultivation medium volume unit. We studied the morphology of the producer’s wild type and mutant cells by means of atomic force microscopy (AFM) (See Fig. 8). The structural organization of the produced films and gel was revealed by means of scanning electron microscopy (SEM) performed after freeze-drying. The composition of the fibers was checked acquiring FTIR Spectroscopy. We established that G. hansenii GH 1/2008 produces a dense film on media containing fructose, glucose and sucrose, while the polymer has gel consistence when grown on maltose, galactose and lactose (See Fig. 1). The maximal quantity (a.d.w.) of polymer was produced on fructose- and sucrose-containing media. The overall number of immobilized producer cells was considerably higher when grown on media with glucose, fructose and sucrose than on gels grown on those containing maltose, galactose and lactose (See Table 1). SEM imaging revealed considerable difference in the microscale organization of films and gels produced by G. hansenii GH 1/2008 on various carbon sources (See Fig. 2). Fructose-containing medium yields the densest structure with dense layers separated by 2μm thick areas filled with non-ordered BC fibrils. The microscale organization of sucrose- and glucose-based films were very similar and had a cell-like structure. In cases where the synthesized polymer had squeezable gel consistence, its microstructure was not layered but close to isotropic. The studies of gels by means of FTIR spectroscopy showed that the gels are also formed of BC molecules; the spectra were almost identical (See Fig. 4). The only difference, i.e. the intensity of the 1638 см-1 peak, can be explained by the presence of a higher amount of bound water in the latter. It is known that some strains of this species may produce glucuronic acid oligomers under unfavorable conditions, but peaks corresponding to carboxyl or carbonyl groups were not revealed in the spectra. This is the evidence that no detectable amounts of glucuronic acid were produced under conditions studied. The analysis of colonies of G. hansenii GH 1/2008 cultivated under static conditions on media containing various carbon sources revealed colonies with two dominating phenotypes: non-mucoid smooth convex colonies and mucoid flat ones (See Fig. 5). The number of cells forming smooth non-mucoid colonies on agarized media was maximal in the inoculations of cultural liquids after the cultivation on media containing fructose and sucrose, i.e. those carbon sources that demonstrated high productivity per 1L of cultural liquid (See Fig. 6). In the inoculations of the cultural liquid and wash-offs of cells immobilized on gels obtained by the cultivation on media containing galactose and lactose, the number of mucoid colonies was considerably higher (See Table 2). The clones forming mucoid type colonies did not produce BC films when reinoculated in liquid media, while those forming colonies of mucoid (smooth) type produce films on the 3rd day of cultivation (See Fig. 7). The analysis of cells shape and sizes by means of AFM did not reveal any statistically valid difference between the mutants and the wild type. The present research shows that the source of carbon is a selective factor in the formation of the inner composition of the population of clones of the bacterial cellulose producer Gluconacetobacter hansenii GH 1/2008. The proliferation of cellulosenegative cells arouses competition for the substrate with cellulose-positive cells of G. hansenii GH 1/2008 that reduces the number of the latter and the production of the exopolymer.


Author(s):  
Abdul Mukheem ◽  
M. Murad Hossain ◽  
Syed Shahabuddin ◽  
Kasturi Muthoosamy ◽  
Sivakumar Manickam ◽  
...  

A wide variety of bacteria are found to be the tiny factories in the production of polyhydroxyalkanoate (PHA) biopolymer. PHA is the polyesters of 3-hydroxyalkanoic acids which occur in bacteria when the bacteria is subjected to nutrient limitation and simultaneously fed with an excess amount of carbon. This unfavorable condition forces the bacteria to store carbon in the form of resorbable cellular inclusions called PHA. Biosynthesized PHA has the ability to replace the currently feasible harmful petroleum based plastics to biobased plastics. PHA research is being focused mainly on two facts - bulk production of environment friendly low-cost PHA and functional group modification for multiple applications to mankind. Many companies are already producing PHA with highly tunable properties and are looking into economically feasible technologies for mass production of PHA. The core focus of PHA research includes a selection of potential PHA producers and low to zero cost carbon sources such as carbon containing wastages of household, farms and industries. This challenge of “trash to treasure” still remains to attain. Tunable properties of PHA have made them a more interesting biomaterial to blend with suitable biopolymers including bioactive compounds. Under precise physiological environment, PHA blends can deliver promising mechanical properties, acting as effective drug carriers and showing time bound degradation. Perhaps desirably tuned PHA may address many health issues including orthopedics - load bearing cartilage, artificial membranes for kidneys, heart and wound management. PHA has high immunotolerance, low toxicity and sustained biodegradability, which have attracted diverse scientist with many medical advancements such as bioabsorbable sutures and 3D structures. In the near future, it is expected to derive many smart auto controllable products from PHA such as microsphere, which could be utilised for a range of applications much more than just drug delivery. Furthermore, naturally produced hybrid PHA will be an interesting candidate as they possess essential properties for targeted applications without further artificial blending or incorporating any components.


2010 ◽  
Vol 432 (2) ◽  
pp. 343-352 ◽  
Author(s):  
Keiji Mitsui ◽  
Masafumi Matsushita ◽  
Hiroshi Kanazawa

Organelle-localized NHEs (Na+/H+ exchangers) are found in cells from yeast to humans and contribute to organellar pH regulation by exporting H+ from the lumen to the cytosol coupled to an H+ gradient established by vacuolar H+-ATPase. The mechanisms underlying the regulation of organellar NHEs are largely unknown. In the present study, a yeast two-hybrid assay identified Mth1p as a new binding protein for Nhx1p, an organellar NHE in Saccharomyces cerevisiae. It was shown by an in vitro pull-down assay that Mth1p bound to the hydrophilic C-terminal half of Nhx1p, especially to the central portion of this region. Mth1p is known to bind to the cytoplasmic domain of the glucose sensor Snf3p/Rgt2p and also functions as a negative transcriptional regulator. Mth1p was expressed in cells grown in a medium containing galactose, but was lost (possibly degraded) when cells were grown in medium containing glucose as the sole carbon source. Deletion of the MTH1 gene increased cell growth compared with the wild-type when cells were grown in a medium containing galactose and with hygromycin or at an acidic pH. This resistance to hygromycin or acidic conditions was not observed for cells grown with glucose as the sole carbon source. Gene knockout of NHX1 increased the sensitivity to hygromycin and acidic pH. The increased resistance to hygromycin was reproduced by truncation of the Mth1p-binding region in Nhx1p. These results implicate Mth1p as a novel regulator of Nhx1p that responds to specific extracellular carbon sources.


2005 ◽  
Vol 19 (11) ◽  
pp. 1401-1408 ◽  
Author(s):  
Christina Biasi ◽  
Olga Rusalimova ◽  
Hildegard Meyer ◽  
Christina Kaiser ◽  
Wolfgang Wanek ◽  
...  

2021 ◽  
Vol 7 (6) ◽  
pp. 409
Author(s):  
Thanaporn Laothanachareon ◽  
Lyon Bruinsma ◽  
Bart Nijsse ◽  
Tom Schonewille ◽  
Maria Suarez-Diez ◽  
...  

Aspergillus niger is the major industrial citrate producer worldwide. Export as well as uptake of citric acid are believed to occur by active, proton-dependent, symport systems. Both are major bottlenecks for industrial citrate production. Therefore, we assessed the consequences of deleting the citT gene encoding the A. niger citrate exporter, effectively blocking active citrate export. We followed the consumption of glucose and citrate as carbon sources, monitored the secretion of organic acids and carried out a thorough transcriptome pathway enrichment analysis. Under controlled cultivation conditions that normally promote citrate secretion, the knock-out strain secreted negligible amounts of citrate. Blocking active citrate export in this way led to a reduced glucose uptake and a reduced expression of high-affinity glucose transporter genes, mstG and mstH. The glyoxylate shunt was strongly activated and an increased expression of the OAH gene was observed, resulting in a more than two-fold higher concentration of oxalate in the medium. Deletion of citT did not affect citrate uptake suggesting that citrate export and citrate uptake are uncoupled from the system.


2002 ◽  
Vol 46 (1-2) ◽  
pp. 519-524 ◽  
Author(s):  
K.R. Pagilla ◽  
A. Sood ◽  
H. Kim

Gordonia amarae, a filamentous actinomycete, commonly found in foaming activated sludge wastewater treatment plants was investigated for its biosurfactant production capability. Soluble acetate and sparingly soluble hexadecane were used as carbon sources for G. amarae growth and biosurfactant production in laboratory scale batch reactors. The lowest surface tension (critical micelle concentration, CMC) of the cell-free culture broth was 55 dynes/cm when 1,900 mg/L acetate was used as the sole carbon source. The lowest surface tension was less than 40 dynes/cm when either 1% (v/v) hexadecane or a mixture of 1% (v/v) hexadecane and 0.5% (w/v) acetate was used as the carbon source. The maximum biomass concentration (the stationary phase) was achieved after 4 days when acetate was used along with hexadecane, whereas it took about 8 days to achieve the stationary phase with hexadecane alone. The maximum biosurfactant production was 3 × CMC with hexadecane as the sole carbon source, and it was 5 × CMC with the mixture of hexadecane and acetate. Longer term growth studies (∼ 35 days of culture growth) indicated that G. amarae produces biosurfactant in order to solubilize hexadecane, and that adding acetate improves its biosurfactant production by providing readily degradable substrate for initial biomass growth. This research confirms that the foaming problems in activated sludge containing G. amarae in the activated sludge are due to the biosurfactant production by G. amarae when hydrophobic substrates such as hexadecane are present.


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