Assessment of thraustochytrids potential for carotenoids, terpenoids and polyunsaturated fatty acids biorefinery

Heterotrophic fast-growing thraustochytrids have been identified as promising candidates for the bioconversion of organic sources into industrially important valuable products. Marine thraustochytrids exhibit remarkable potential for high-value polyunsaturated fatty acids (PUFAs) production however their potential is recently discovered for high-value carotenoids and terpenoids which also have a role as a dietary supplement and health promotion. Primarily, omega-3 and 6 PUFAs (DHA, EPA, and ARA) from thraustochytrids are emerging sources of nutrient supplements for vegetarians replacing animal sources and active pharmaceutical ingredients due to excellent bioactivities. Additionally, thraustochytrids produce reasonable amounts of squalene (terpenoid) and carotenoids which are also high-value products with great market potential. Hence, these can be coextracted as a byproduct with PUFAs under the biorefinery concept. There is still quite a few printed information on bioprocess conditions for decent (co)-production of squalene and carotenoid from selective protists such as lutein, astaxanthin, canthaxanthin, and lycopene. The current review seeks to provide a concise overview of the coproduction and application of PUFAs, carotenoids, and terpenoids from oleaginous thraustochytrids and their application to human health.

Advances in Algomics technology: Application in wastewater treatment and biofuel production

Advanced sustainable bioremediation is gaining importance with rising global pollution. This review examines microalgae's potential for sustainable bioremediation and process enhancement using multi-omics approaches. Recently, microalgae-bacterial consortia have emerged for synergistic nutrient removal, allowing complex metabolite exchanges. Advanced bioremediation requires effective consortium design or pure culture based on the treatment stage and specific roles. The strain potential must be screened using modern omics approaches aligning wastewater composition. The review highlights crucial research gaps in microalgal bioremediation. It discusses multi-omics advantages for understanding microalgal fitness concerning wastewater composition and facilitating the design of microalgal consortia based on bioremediation skills. Metagenomics enables strain identification, thereby monitoring microbial dynamics during the treatment process. Transcriptomics and metabolomics encourage the algal cell response toward nutrients and pollutants in wastewater. Multi-omics role is also summarized for product enhancement to make algal treatment sustainable and fit for sustainable development goals and growing circular bioeconomy scenario.

Technological advancements in valorization of second generation (2G) feedstocks for bio-based succinic acid production

Succinic acid (SA) is used as a commodity chemical and as a precursor in chemical industry to produce other derivatives such as 1,4-butaneidol, tetrahydrofuran, fumaric acid, and bio-polyesters. The production of bio-based SA from renewable feedstocks has always been in the limelight owing to the advantages of renewability, abundance and reducing climate change by CO₂ capture. Considering this, the current review focuses on various 2G feedstocks such as lignocellulosic biomass, crude glycerol, and food waste for cost-effective SA production. It also highlights the importance of producing SA via separate enzymatic hydrolysis and fermentation, simultaneous saccharification and fermentation, and consolidated bioprocessing. Furthermore, recent advances in genetic engineering, and downstream SA processing are thoroughly discussed. It also elaborates on the techno-economic analysis and life cycle assessment (LCA) studies carried out to understand the economics and environmental effects of bio-based SA synthesis.

Cold-adaptive traits identified by comparative genomic analysis of a lipase-producing Pseudomonas sp. HS6 isolated from snow-covered soil of Sikkim Himalaya and molecular simulation of lipase for wide substrate specificity

The genomic analysis of industrially important bacteria can help in understanding their capability to withstand extreme environments and shed light on their metabolic capabilities. The whole genome of a previously reported broad temperature active lipase-producing Pseudomonas sp. HS6, isolated from snow-covered soil of the Sikkim Himalayan Region, was analyzed to understand the capability of the bacterium to withstand cold temperatures and study its lipolytic nature. Pseudomonas sp. HS6 was found to be psychrotolerant with an optimal growth temperature ranging between 25 and 30 °C, with the ability to grow at 5 °C. The genome harbours various cold-adaptation genes, such as cold-shock proteins, fatty acid alteration, and cold stress-tolerance genes, supporting the psychrotolerant nature of the organism. The comparative analysis of Pseudomonas sp. HS6 genome showed the presence of amino acid substitutions in genes that favor efficient functioning and flexibility at cold temperatures. Genome mining revealed the presence of four triacylglycerol lipases, among which the putative lipase 3 was highly similar to the broad temperature-active lipase purified and characterized in our previous study. In silico studies of putative lipase 3 revealed broad substrate specificity with partial and no inhibition of the enzyme activity in the presence of PMSF and orlistat. The presence of genes associated with cold adaptations and true lipases with activity at broad temperature and substrate specificity in the genome of Pseudomonas sp. HS6 makes this bacterium a suitable candidate for industrial applications.

High level xylitol production by Pichia fermentans using non-detoxified xylose-rich sugarcane bagasse and olive pits hydrolysates

Hemicellulosic sugars, the overlooked fraction of lignocellulosic residues can serve as potential and cost-effective raw material that can be exploited for xylitol production. Xylitol is a top platform chemical with applications in food and pharmaceutical industries. Sugarcane bagasse (SCB) and olive pits (OP) are the major waste streams from sugar and olive oil industries, respectively. The current study evaluated the potential of Pichia fermentans for manufacturing of xylitol from SCB and OP hydrolysates through co-fermentation strategy. The highest xylitol accumulation was noticed with a glucose and xylose ratio of 1:10 followed by feeding with xylose alone. The fed-batch cultivation using pure xylose, SCB, and OP hydrolysates, resulted in xylitol accumulation of 102.5, 86.6 and 71.9 g/L with conversion yield of 0.78, 0.75 and 0.74 g/g, respectively. The non-pathogenic behaviour and ability to accumulate high xylitol levels from agro-industrial residues demonstrates the potential of P. fermentans as microbial cell factory.

High yield recovery of 2,3-butanediol from fermented broth accumulated on xylose rich sugarcane bagasse hydrolysate using aqueous two-phase extraction system

Downstream processing of chemicals obtained from fermentative route is challenging and cost-determining factor of any bioprocess. 2,3-Butanediol (BDO) is a promising chemical building block with myriad applications in the polymer, food, pharmaceuticals, and fuel sector. The current study focuses on the recovery and purification of BDO produced (68.2 g/L) from detoxified xylose-rich sugarcane bagasse hydrolysate by a mutant strain of Enterobacter ludwigii. Studies involving screening and optimization of aqueous-two phase system (ATPS) revealed that 30% w/v (NH₄)₂SO₄ addition to clarified fermented broth facilitated BDO extraction in isopropanol (0.5 v/v), with maximum recovery and partition coefficient being 97.9 ± 4.6% and 45.5 ± 3.5, respectively. The optimized protocol was repeated with unfiltered broth containing 68.2 g/L BDO, cell biomass, and unspent protein, which led to the partitioning of 66.7 g/L BDO, 2.0 g/L xylose and 9.0 g/L acetic acid into organic phase with similar BDO recovery (97%) and partition coefficient (45).

Production and characterisation of lipase for application in detergent industry from a novel Pseudomonas helmanticensis HS6

The aim of this study was to explore novel source of lipase from biodiversity hot spot region of Sikkim with activity at broad temperature range for application in detergent industry. Among the isolates, Pseudomonas helmanticensis HS6 showed activity at wide range of temperatures was selected for lipase production. Statistical optimisation for enhanced production of lipase resulted in enhancement of lipase activity from 2.3 to 179.3 U/mg. Lipase was purified resulting in 18.78 fold purification, 5.58% yield and high specific activity of 3368 U/mg. The partially purified lipase was found to be active in wide range of temperature (5-80 °C) and pH (6-9), showing optimum activity at 50 °C at pH 7. Peptide sequences on mass spectrometric analysis of purified lipase showed similarity to lipase family protein of three species of Pseudomonas. Both crude and purified lipase retained residual activity of 40-80% after 3 h of incubation with commercial detergents suggesting its application in detergent industry.

Pretreatment strategies for enhanced biogas production from lignocellulosic biomass

The inclusion of a pretreatment step in anaerobic digestion processes increases the digestibility of lignocellulosic biomass and enhances biogas yields by promoting lignin removal and the destruction of complex biomass structures. The increase in surface area enables the efficient interaction of microbes or enzymes, and a reduction in cellulose crystallinity improves the digestion process under anaerobic conditions. The pretreatment methods may vary based on the type of the lignocellulosic biomass, the nature of the subsequent process and the overall economics of the process. An improved biogas production by 1200% had been reported when ionic liquid used as pretreatment strategy for anaerobic digestion. The different pretreatment techniques used for lignocellulosic biomasses are generally grouped into physical, chemical, physicochemical, and biological methods. These four modes of pretreatment on lignocellulosic biomass and their impact on biogas production process is the major focus of this review article.

Optimization of Process Parameters for the Production of γ-Linolenic Acid by Cunninghamella elegans CFR C07 in Submerged Fermentation

The production of γ-linolenic acid (GLA) by the fungus Cunninghamella elegans CFR C07 in submerged fermentation was studied. Culture parameters such as carbon source and incubation time were optimized. Four different extraction methods using solvents with acid washed sand, glass beads, lyophilization and Soxhlet extraction were evaluated for improved extraction of lipids from the fungal biomass after fermentation. The GLA production was initially optimized in 250-mL flask and the process was demonstrated in a 3-litre fermentor. The maximum GLA production was 882 mg/L in shake flask culture and 733 mg/L in the fermentor. The study shows that Cunninghamella elegans CFR C07 is a potent organism for the production of GLA under submerged conditions.

Production of Pectinase from Bacillus sonorensis MPTD1

Seven isolates from spoiled fruits and vegetables were screened for pectinase production using pectin agar plates and the most efficient bacterial strain, MPTD1, was identified as Bacillus sonorensis. Optimisation of various process parameters was done using Plackett-Burman and Box-Behnken designs and it was found that parameters like yeast extract, K₂HPO₄, incubation time, NaNO₃ and KCl have a negative impact on pectinase production. Parameters like pH and MgSO₄ and pectin mass fractions have a positive impact on pectinase production. The maximum obtained enzyme activity was 2.43 (μM/mL)/min. This is the first report on pectinase production by Bacillus sonorensis.

Applications of Microbial Enzymes in Food Industry

The use of enzymes or microorganisms in food preparations is an age-old process. With the advancement of technology, novel enzymes with wide range of applications and specificity have been developed and new application areas are still being explored. Microorganisms such as bacteria, yeast and fungi and their enzymes are widely used in several food preparations for improving the taste and texture and they offer huge economic benefits to industries. Microbial enzymes are the preferred source to plants or animals due to several advantages such as easy, cost-effective and consistent production. The present review discusses the recent advancement in enzyme technology for food industries. A comprehensive list of enzymes used in food processing, the microbial source of these enzymes and the wide range of their application are discussed.

Production of chitin deacetylase by Aspergillus flavus in submerged conditions

Chitosan is a biopolymer obtained by deacetylation of chitin and has been proven to have various applications in industry and biomedicine. Deacetylation of chitin using the enzyme chitin deacetylase (CDA) is favorable in comparison to the hazardous chemical method involving strong alkali and high temperature. A fungal strain producing CDA was isolated from environmental samples collected from coastal regions of South Kerala, India. It was identified as Aspergillus flavus by morphological characteristics and ITS DNA analysis. Nutritional requirement for maximum production of CDA under submerged condition was optimized using statistical methods including Plackett-Burman and response surface methodology central composite design. A 5.98-fold enhancement in CDA production was attained in shake flasks when the fermentation process parameters were used at their optimum levels. The highest CDA activity was 57.69 ± 1.68 U under optimized bioprocess conditions that included 30 g L(-1) glucose, 40 g L(-1) yeast extract, 15 g L(-1) peptone, and 7 g L(-1) MgCl2 at initial media pH of 7 and incubation temperature of 32°C after 48 hr of incubation, while the unoptimized basal medium yielded 9.64 ± 2.04 U.

Application of a new xylanase activity from Bacillus amyloliquefaciens XR44A in brewer's spent grain saccharification

BACKGROUND

Cellulases and xylanases are the key enzymes involved in the conversion of lignocelluloses into fermentable sugars. Western Ghat region (India) has been recognized as an active hot spot for the isolation of new microorganisms. The aim of this work was to isolate new microorganisms producing cellulases and xylanases to be applied in brewer's spent grain saccharification.

RESULTS

93 microorganisms were isolated from Western Ghat and screened for the production of cellulase and xylanase activities. Fourteen cellulolytic and seven xylanolytic microorganisms were further screened in liquid culture. Particular attention was focused on the new isolate Bacillus amyloliquefaciens XR44A, producing xylanase activity up to 10.5 U mL^-1. A novel endo-1,4-beta xylanase was identified combining zymography and proteomics and recognized as the main enzyme responsible for B. amyloliquefaciens XR44A xylanase activity. The new xylanase activity was partially characterized and its application in saccharification of brewer's spent grain, pretreated by aqueous ammonia soaking, was investigated.

CONCLUSION

The culture supernatant of B. amyloliquefaciens XR44A with xylanase activity allowed a recovery of around 43% xylose during brewer's spent grain saccharification, similar to the value obtained with a commercial xylanase from Trichoderma viride, and a maximum arabinose yield of 92%, around 2-fold higher than that achieved with the commercial xylanase. © 2014 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Dilute acid pretreatment and enzymatic hydrolysis of sorghum biomass for sugar recovery--a statistical approach

Sorghum is one of the commercially feasible lignocellulosic biomass and has a great potential of being sustainable feedstock for renewable energy. As with any lignocellulosic biomass, sorghum also requires pretreatment which increases its susceptibility to hydrolysis by enzymes for generating sugars which can be further fermented to alcohol. In the present study, sorghum biomass was evaluated for deriving maximum fermentable sugars by optimizing various pretreatment parameters using statistical optimization methods. Pretreatment studies were done with H2SO4, followed by enzymatic saccharification. The efficiency of the process was evaluated on the basis of production of the total reducing sugars released during the process. Compositional analysis was done for native as well as pretreated biomass and compared. The biomass pretreated with the optimized conditions could yield 0.408 g of reducing sugars /g of pretreated biomass upon enzymatic hydrolysis. The cellulose content in the solid portion obtained after pretreatment using optimised conditions was found to be increased by 43.37% with lesser production of inhibitors in acid pretreated liquor.

Abstract P3-04-06: Damage-induced BRCA1 phosphorylation contributes to the timing of end resection

Germline mutations of BRCA1 predispose women to breast and ovarian cancers. BRCA1 functions as a tumor suppressor. A wealth of evidence has established that BRCA1 plays an important role in DNA repair and cell cycle checkpoint control. Efficient repair of double-strand-breaks (DSBs) by BRCA1 is essential to its tumor suppression function. DSBs can be repaired either by homologous recombination (HR) or by nonhomologous end-joining (NHEJ). BRCA1 is hyperphosphorylated upon DSBs. Although phosphorylation of BRCA1 is among the earliest events documented upon DNA damage, the role of BRCA1 phosphorylation in DNA repair remains unclear after more than a decade. It has been proposed that BRCA1 serves as a scaffolding protein that recruits multiple repair proteins to the break sites. One of the BRCA1-containing complexes, MRN (Mre11-Rad50-Nbs1)-BRCA1-CtIP, promotes HR repair by initiating DNA end-resection, the first step in the HR pathway. Mre11 possesses intrinsic nuclease activity, which likely facilitates initial processing of DNA ends for subsequent extensive end-resection. Believed to stimulate the nuclease activity of the MRN complex, CtIP is recruited to the complex by BRCA1.

In spite of these useful molecular models, the precise function of BRCA1 in DSB repair, especially the role of its phosphorylation, remains elusive. BRCA1 is phosphorylated by Chk2 kinase upon g-irradiation at serine 988 (human) or serine 971 (mouse). Our data shows that a point mutation in mouse BRCA1 (S971A) that abolishes the Chk2 phosphorylation site impairs end-resection after DSBs. The S971A mutation does not appear to affect the assembly of MRN and CtIP at DSBs, but specifically delays dispersion of BRCA1 from DSBs. Interestingly, BRCA1 is ubiquitinated and degraded by SCFSkp2, and loss of Chk2 phosphorylation at S988 of human BRCA1 impairs its ubiquitination. Previous work has revealed BRCA1 as a scaffold protein for the assembly of HR proteins at DSBs. Paradoxically, BRCA1 also inhibits Mre11 nuclease activity. Our study suggests that BRCA1 plays a dual role in HR. Although BRCA1 is required for initial assembly of the MRN-BRCA1-CtIP complex at DSBs, the exit of BRCA1 from the MRN-BRCA1-CtIP complex is required to relieve its inhibitory effect on Mre11 nuclease activity. Mechanistically, this critical “exit” of BRCA1 from the MRN-BRCA1-CtIP complex is regulated through phosphorylation catalyzed by Chk2 and then degraded by SCFSkp2, which is expressed at S/G2 phases, thus ensuring the initiation of end resection/HR to S/G2 phases of the cell cycle. Our study explains two seemingly paradoxical observations: BRCA1 is required for assembly of the MRN-BRCA1-CtIP complex, but it inhibits Mre11 nuclease activity required for end-resection.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-04-06.

Biobutanol production from rice straw by a non acetone producing Clostridium sporogenes BE01

Biobutanol from lignocellulosic biomass has gained much attention due to several advantages over bioethanol. Though microbial production of butanol through ABE fermentation is an established technology, the use of lignocellulosic biomass as feedstock presents several challenges. In the present study, biobutanol production from enzymatic hydrolysate of acid pretreated rice straw was evaluated using Clostridium sporogenes BE01. This strain gave a butanol yield of 3.43 g/l and a total solvent yield of 5.32 g/l in rice straw hydrolysate supplemented with calcium carbonate and yeast extract. Hydrolysate was analyzed for the level of inhibitors such as acetic acid, formic acid and furfurals which affect the growth of the organism and in turn ABE fermentation. Methods for preconditioning the hydrolysate to remove toxic end products were done so as to improve the fermentation efficiency. Conditions of ABE fermentation were fine tuned resulting in an enhanced biobutanol reaching 5.52 g/l.

Conditions providing enhanced transfection efficiency in rat pheochromocytoma PC12 cells permit analysis of the activity of the far-upstream and proximal promoter of the brain creatine kinase gene

While brain creatine kinase (CKB) is expressed at highest levels in the brain, where it functions in regenerating ATP, the gene elements and protein factors regulating CKB transcription in neuronal and glial cells have not been identified. To investigate the regulation of CKB in neuronal cells, we examined the expression of the promoter proximal and 5' far-upstream regions of the rat CKB gene transiently transfected into rat PC12 pheochromocytoma cells. Initially, these experiments were hampered by the extremely low transfection efficiency of PC12 cells. We increased efficiency by greater than 200-fold by employing CaPO4-precipitated DNA transfection into PC12 cells which were optimized for transient transfection by: (i) culturing cells in polylysine-coated dishes to insure attachment throughout transfection; (ii) exposing cells to transfected DNA for an optimal time and employing a glycerol shock; and, most importantly, (iii) dissociating the characteristic self-adhesive clumps of PC12 into mostly single cells. Use of the plasmid expressing green fluorescent protein allowed identification of the transfected cells that averaged 10-20% of the total. Analyses of CKB promoter-CAT gene constructs showed that in PC12 cells expression of the proximal (0.2 kb) CKB promoter was low while expression of the 1.4 kb promoter was three fold higher and the 2.9 kb promoter was ten fold higher, suggesting the presence of at least two upstream cis-acting, positive regulatory elements. In agreement, the steady-state CKB mRNA level was higher in PC12 than in other neuronal cell lines examined, possibly reflecting the effects of positive upstream factors. The results are discussed in relation to how this economical and straightforward transfection procedure may be useful in identify factors regulating the transcription of CKB and other genes expressed in neuronal cells.

Expression of the rat brain creatine kinase gene in C6 glioma cells

We have recently shown that while brain creatine kinase (CKB) mRNA was detectable in RNA from cultured primary rat brain neurons, CKB mRNA was about 15-fold higher in primary astrocytes and 17-fold higher in oligodendrocytes (Molloy et al., J Neurochem 59:1925-1932, 1992). To begin to understand the molecular mechanisms responsible for brain glial cells containing the highest levels of CKB mRNA in the body, we have examined the expression of rat CKB mRNA in established C6 glioma cells. RNase-protection analysis showed the endogenous CKB mRNA levels in exponentially growing C6 were high and measured 50% of that in total RNA from rat brain lysate and 60% of that in cultured primary astrocytes and oligodendrocytes. The 5' and 3' ends of CKB mRNA in C6 were mapped to the same nucleotides as CKB mRNA from rat brain, indicating that the sites of in vivo transcription initiation and termination/polyadenylation of CKB mRNA in C6 are the same as in total rat brain RNA. The level of CKB enzyme activity in C6 whole cell lysates was among the highest of the glial cell lines which we measured. All creatine kinase enzyme activity present in C6 was found in the dimeric CKB isoform (BB), which is characteristic of CKB expression in the brain. A 2.9 kb gene fragment containing the basal CKB promoter and far-upstream 5' sequences was cloned upstream of the chloramphenicol acetyltransferase (CAT) gene and transfected into C6 cells. CAT activity was readily detectable in C6 and mapping of the 5' end of the CAT mRNA showed that transcription was directed from the correct initiation site. Since we found C6 cells were difficult to transfect, conditions were established which both maximized transfection efficiency and maintained normal C6 cell morphology. These results should permit the future identification of the nuclear trans-acting factors and the cognate cis-acting regulatory elements responsible for high CKB mRNA expression in brain glial cells.