Microbial production of N-acetyl-D-glucosamine (GlcNAc) for versatile applications: Biotechnological strategies for green process development

N-acetyl-d-glucosamine (GlcNAc) is a commercially important amino sugar for its wide range of applications in pharmaceutical, food, cosmetics and biofuel industries. In nature, GlcNAc is polymerised into chitin biopolymer, which is one of the major constituents of fungal cell wall and outer shells of crustaceans. Sea food processing industries generate a large volume of chitin as biopolymeric waste. Because of its high abundance, chitinaceous shellfish wastes have been exploited as one of the major precursor substrates of GlcNAc production, both in chemical and enzymatic means. Nevertheless, the current process of GlcNAc extraction from shellfish wastes generates poor turnover and attracts environmental hazards. Moreover, GlcNAc isolated from shellfish could not be prescribed to certain groups of people because of the allergic nature of shell components. Therefore, an alternative route of GlcNAc production is advocated. With the advancement of metabolic construction and synthetic biology, microbial synthesis of GlcNAc is gaining much attention nowadays. Several new and cutting-edge technologies like substrate co-utilization strategy, promoter engineering, and CRISPR interference system were proposed in this fascinating area. The study would put forward the potential application of microbial engineering in the production of important pharmaceuticals. Very recently, autotrophic fermentation of GlcNAc synthesis has been proposed. The metabolic engineering approaches would offer great promise to mitigate the issues of low yield and high production cost, which are major challenges in microbial bio-processes industries. Further process optimization, optimising metabolic flux, and efficient recovery of GlcNAc from culture broth, should be investigated in order to achieve a high product titer. The current study presents a comprehensive review on microbe-based eco-friendly green methods that would pave the way towards the development of future research directions in this field for the designing of a cost-effective fermentation process on an industrial setup.

Potential utility of bacterial protein nanoreactor for sustainable in-situ biocatalysis in wide range of bioprocess conditions

Bacterial microcompartments (MCPs) are proteinaceous organelles that natively encapsulates the enzymes, substrates, and cofactors within a protein shell. They optimize the reaction rates by enriching the substrate in the vicinity of enzymes to increase the yields of the product and mitigate the outward diffusion of the toxic or volatile intermediates. The shell protein subunits of MCP shell are selectively permeable and have specialized pores for the selective inward diffusion of substrates and products release. Given their attributes, MCPs have been recently explored as potential candidates as subcellular nano-bioreactor for the enhanced production of industrially important molecules by exercising pathway encapsulation. In the current study, MCPs have been shown to sustain enzyme activity for extended periods, emphasizing their durability against a range of physical challenges such as temperature, pH and organic solvents. The significance of an intact shell in conferring maximum protection is highlighted by analyzing the differences in enzyme activities inside the intact and broken shell. Moreover, a minimal synthetic shell was designed with recruitment of a heterologous enzyme cargo to demonstrate the improved durability of the enzyme. The encapsulated enzyme was shown to be more stable than its free counterpart under the aforementioned conditions. Bacterial MCP-mediated encapsulation can serve as a potential strategy to shield the enzymes used under extreme conditions by maintaining the internal microenvironment and enhancing their cycle life, thereby opening new means for stabilizing, and reutilizing the enzymes in several bioprocess industries.

Observational studies on the efficacy of carbamazepine and ascorbyl palmitate in managing trigeminal neuralgia

OBJECTIVE

Ascorbyl palmitate is a fat-soluble ester of vitamin C and is used as an antioxidant food additive. While literature reports that ascorbyl palmitate can prevent exacerbation of pain and improve the quality of life of patients suffering from pain, this is not yet supported by clinical trial data. Our study aimed to investigate the effectiveness of ascorbyl palmitate in managing trigeminal neuralgia.

PATIENTS AND METHODS

This study was carried out in a single-centre clinical trial in which subjects suffering from trigeminal neuralgia (N=11) were included. All patients were on carbamazepine when first included and, after washout period, received Ascorbyl palmitate. Eligible patients had the most severe trigeminal neuralgia pain in the oral cavity or pain on touching trigger zones, aged 20 years or older, were capable of proper assessment of the severity of pain and their condition, and had experienced multiple episodes of intraoral pain for at least 3 months with a pain intensity of more than 4 points on the numerical rating scale. The Brief Pain Questionnaire was used to evaluate patient's quality of life.

RESULTS

A total of 11 patients were included with a mean age 55.36±10.67 years (7 males, 4 females). Most patients had compression by the superior cerebellar artery and vascular loops upon magnetic resonance examination. The mean numerical rating scale score for carbamazepine after one month was 7.9±0.56 (95% CI 7.49, 8.30). Similarly, for ascorbyl palmitate was 5.5±1.50 (95% CI 4.42, 6.57) (p<0.001).

CONCLUSIONS

Ascorbyl palmitate can be used as an adjunct intervention in managing trigeminal neuralgia pain. According to the results, ascorbyl palmitate prevents frequent exacerbation of pain and improves patient quality of life.

Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella

Bacterial microcompartments (MCPs) are protein-based organelles that consist of metabolic enzymes encapsulated within a protein shell. The function of MCPs is to optimize metabolic pathways by increasing reaction rates and sequestering toxic pathway intermediates. A substantial amount of effort has been directed toward engineering synthetic MCPs as intracellular nanoreactors for the improved production of renewable chemicals. A key challenge in this area is engineering protein shells that allow the entry of desired substrates. In this study, we used site-directed mutagenesis of the PduT shell protein to remove its central iron-sulfur cluster and create openings (pores) in the shell of the Pdu MCP that have varied chemical properties. Subsequently, in vivo and in vitro studies were used to show that PduT-C38S and PduT-C38A variants increased the diffusion of 1,2-propanediol, propionaldehyde, NAD⁺ and NADH across the shell of the MCP. In contrast, PduT-C38I and PduT-C38W eliminated the iron-sulfur cluster without altering the permeability of the Pdu MCP, suggesting that the side-chains of C38I and C38W occluded the opening formed by removal of the iron-sulfur cluster. Thus, genetic modification offers an approach to engineering the movement of larger molecules (such as NAD/H) across MCP shells, as well as a method for blocking transport through trimeric bacterial microcompartment (BMC) domain shell proteins.

The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene

Bacterial microcompartments (MCPs) are complex organelles that consist of metabolic enzymes encapsulated within a protein shell. In this study, we investigate the function of the PduJ MCP shell protein. PduJ is 80% identical in amino acid sequence to PduA and both are major shell proteins of the 1,2-propanediol (1,2-PD) utilization (Pdu) MCP of Salmonella. Prior studies showed that PduA mediates the transport of 1,2-PD (the substrate) into the Pdu MCP. Surprisingly, however, results presented here establish that PduJ has no role 1,2-PD transport. The crystal structure revealed that PduJ was nearly identical to that of PduA and, hence, offered no explanation for their differential functions. Interestingly, however, when a pduJ gene was placed at the pduA chromosomal locus, the PduJ protein acquired a new function, the ability to mediate 1,2-PD transport into the Pdu MCP. To our knowledge, these are the first studies to show that that gene location can determine the function of a MCP shell protein. We propose that gene location dictates protein-protein interactions essential to the function of the MCP shell.

A putative low-molecular-mass penicillin-binding protein (PBP) of Mycobacterium smegmatis exhibits prominent physiological characteristics of DD-carboxypeptidase and beta-lactamase

DD-carboxypeptidases (DD-CPases) are low-molecular-mass (LMM) penicillin-binding proteins (PBPs) that are mainly involved in peptidoglycan remodelling, but little is known about the dd-CPases of mycobacteria. In this study, a putative DD-CPase of Mycobacterium smegmatis, MSMEG_2433 is characterized. The gene for the membrane-bound form of MSMEG_2433 was cloned and expressed in Escherichia coli in its active form, as revealed by its ability to bind to the Bocillin-FL (fluorescent penicillin). Interestingly, in vivo expression of MSMEG_2433 could restore the cell shape oddities of the septuple PBP mutant of E. coli, which was a prominent physiological characteristic of DD-CPases. Moreover, expression of MSMEG_2433 in trans elevated beta-lactam resistance in PBP deletion mutants (ΔdacAdacC) of E. coli, strengthening its physiology as a dd-CPase. To confirm the biochemical reason behind such physiological behaviours, a soluble form of MSMEG_2433 (sMSMEG_2433) was created, expressed and purified. In agreement with the observed physiological phenomena, sMSMEG_2433 exhibited DD-CPase activity against artificial and peptidoglycan-mimetic DD-CPase substrates. To our surprise, enzymic analyses of MSMEG_2433 revealed efficient deacylation for beta-lactam substrates at physiological pH, which is a unique characteristic of beta-lactamases. In addition to the MSMEG_2433 active site that favours dd-CPase activity, in silico analyses also predicted the presence of an omega-loop-like region in MSMEG_2433, which is an important determinant of its beta-lactamase activity. Based on the in vitro, in vivo and in silico studies, we conclude that MSMEG_2433 is a dual enzyme, possessing both DD-CPase and beta-lactamase activities.

Diverse bacterial microcompartment organelles

Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.

Quantitative study of As (V) and As (III) interaction with mangrove DNA by molecular fluorescence spectroscopy

This study describes the in vitro study of (1:1) one step nucleophilic displacement ([Formula: see text]) of phosphate by heavier anion arsenate and arsenite in the DNA of arsenic ridden Sundarban mangroves. Mangrove DNA was found to give rise to a broad fluorescence and its integrated fluorescence intensity was enhanced on addition of As (V) and As (III), respectively. Analyses of the fluorescence parameter showed adequacy of 1:1 model to describe substitution of phosphate of mangrove DNA chain exiplex by arsenate and arsenite with equilibrium constant (log Kc) ranging between 4.19 and 4.32 for As (V), and between 3.77 and 3.89 for As (III) at pH 7 and 25°C. In the cases, the melting temperature (Tm) and reassociation rate constant of mangrove DNA was increased on treatment with As (V) and As (III). It is suggested that heavier ion arsenate and arsenite may substitute phosphate in natural DNA.

Implication of organic matter on arsenic and antimony sequestration in sediment: evidence from Sundarban mangrove forest, India

This study reports the measurement of stability constants for the interaction of As (V and III) and Sb (V and III) with humic substances extracted from aquatic sediments of the Sundarban mangrove forest ecosystem. It was observed that As and Sb formed a slightly more stable association with fulvic acid (FA) than with its humic acid (HA) counterpart. Quenching of fluorescence at increasing As (III and V) or Sb (III and V): FA or HA ratios was obtained that ideally correspond to a 1:1 complexation model. Quite strong complexation of As and Sb by FA and HA occurs at neutral pH, indicating that HA and FA probably markedly affect the mobility of As and Sb in the mangrove environment.

Moderate deacylation efficiency of DacD explains its ability to partially restore beta-lactam resistance in Escherichia coli PBP5 mutant

Of the five dd-carboxypeptidases in Escherichia coli, only PBP5 demonstrates its physiological significance by maintaining cell shape and intrinsic beta-lactam resistance. DacD can partially compensate for the lost beta-lactam resistance in PBP5 mutant, although its biochemical reason is unclear. To understand the mechanism(s) underlying such behaviour, we constructed soluble DacD (sDacD) and compared its biophysical and biochemical properties with those of sPBP5, in vitro. Unlike sPBP6, sDacD can deacylate Bocillin significantly, which is very similar to sPBP5. sDacD shows weak dd-carboxypeptidase activity, although lower than that of sPBP5. Bioinformatics analyses reveal a similar architecture of sPBP5 and sDacD. Therefore, based on the obtained results we can infer that biochemically DacD and PBP5 are more closely related to each other than to PBP6, enabling DacD and PBP5 to play a nearly similar physiological function in terms of recovering the lost beta-lactam resistance.

Virulence factors are released in association with outer membrane vesicles of Pseudomonas syringae pv. tomato T1 during normal growth

Outer membrane vesicles (OMVs) are released from Pseudomonas syringae pv. tomato T1 (Pst T1) during their normal growth. These extracellular compartments are comprised of a complete set of biological macromolecules that includes proteins, lipids, lipopolysaccharides, etc. It is evident from proteomics analyses the OMVs of Pst T1 contain membrane- and virulence-associated proteins. In addition, OMVs of this organism are also associated with phytotoxin, coronatine. Therefore, OMVs of Pst T1 must play a significant role during pathogenicity to host plant. However, further studies are required whether these structures can serve as "vehicles" for the transport of virulence factors into the host membrane.

Wood chemistry and density: an analog for response to the change of carbon sequestration in mangroves

This study aimed to resolve the variations of physical and chemical properties of wood records measured in different mangroves with their annual carbon sequestration. The methods of investigation used were to examine growth rate by monitoring breast height diameter, wood chemistry and density, FTIR spectroscopy and thermogravimetry. Carbon sequestration rate showing an increase with density varied between 0.088 and 0.171 μg C kg(-1) AGB s(-1), and Avicennia marina showed the maximum value and Bruguiera gymnorrhiza, the minimum. The changes in FTIR bands at 4000-2500 cm(-1) and 1700-800 cm(-1) were correlated to the variations in cellulose in mangrove woods and lignin to cellulose ratio ranged between 0.21 and 1.75. Thermal analyses of mangrove wood suggested that the fuel value index (985-3922) exhibited an increase with the decrease in maximum decomposition temperature and density. The seasonal variation of temperature and CO2 were likely to affect chemical properties through changes in wood density.

Differential expression of membrane proteins helps Antarctic Pseudomonas syringae to acclimatize upon temperature variations

Antarctic bacteria are adapted to the extremely low temperature. The transcriptional and translational machineries of these bacteria are adapted to the sub-zero degrees of temperature. Studies directed towards identifying the changes in the protein profiles during changes in the growth temperatures of an Antarctic bacterium Pseudomonas syringae Lz4W may help in understanding the molecular basis of cold adaptation. In this study, subcellular fractionation methods of proteins were used for the enrichment and identification of proteins including low abundance proteins. The membrane proteins of the bacterium P. syringae Lz4W were prepared employing sucrose density gradient method. The proteins were separated through 2D gel-electrophoresis with the pH ranges 3-10, 4-7 and 5-8 using the detergent, amidosulfobetaine (ASB-14). The proteins separated on the 1D SDS PAGE and 2D gels were identified with the help of LC-ESI MS/MS and MALDI TOF TOF using bioinformatic programs MASCOT and SEQUEST. Since the genome sequence of P. syringae Lz4W is not available, the proteins are identified by using the genome database of the Pseudomonas sp. available at NCBI. The present studies focus on identifying temperature dependent expression of proteins by employing LC-MS/MS method and the functional significance of these proteins is discussed.

PBP5, PBP6 and DacD play different roles in intrinsic β-lactam resistance of Escherichia coli

Escherichia coli PBP5, PBP6 and DacD, encoded by dacA, dacC and dacD, respectively, share substantial amino acid identity and together constitute ~50 % of the total penicillin-binding proteins of E. coli. PBP5 helps maintain intrinsic β-lactam resistance within the cell. To test if PBP6 and DacD play simlar roles, we deleted dacC and dacD individually, and dacC in combination with dacA, from E. coli 2443 and compared β-lactam sensitivity of the mutants and the parent strain. β-Lactam resistance was complemented by wild-type, but not dd-carboxypeptidase-deficient PBP5, confirming that enzymic activity of PBP5 is essential for β-lactam resistance. Deletion of dacC and expression of PBP6 during exponential or stationary phase did not alter β-lactam resistance of a dacA mutant. Expression of DacD during mid-exponential phase partially restored β-lactam resistance of the dacA mutant. Therefore, PBP5 dd-carboxypeptidase activity is essential for intrinsic β-lactam resistance of E. coli and DacD can partially compensate for PBP5 in this capacity, whereas PBP6 cannot.

Deletion of penicillin-binding protein 5 (PBP5) sensitises Escherichia coli cells to beta-lactam agents

Escherichia coli penicillin-binding protein 5 (PBP5), a dd-carboxypeptidase encoded by the dacA gene, plays a key role in the maintenance of cell shape. Although PBP5 shares one of the highest copy numbers among the PBPs, it is not essential for cell survival. To determine the effect of this redundant PBP on beta-lactam antibiotic susceptibility, PBP5 was deleted from O-antigen-negative E. coli K-12 (CS109) and O8-antigen-positive E. coli 2443, thus creating strains AM15-1 and AG1O5-1, respectively. Compared with the parent strains, both mutants were four- to eight-fold more susceptible to all the beta-lactam antibiotics tested. Reversion to beta-lactam resistance was observed in the mutants upon complementing with cloned PBP5, indicating the involvement of PBP5 in maintaining an O-antigen-independent intrinsic beta-lactam resistance in E. coli cells. To check whether other dacA homologues were able to substitute this behaviour of E. coli PBP5, AG1O5-1 was complemented with its nearest dacA homologues (Salmonella enterica serovar Typhimurium LT2, Vibrio cholerae and Haemophilus influenzae). All of the cloned homologues were capable of restoring the lost beta-lactam resistance in AG1O5-1, either completely or at least partially. Therefore, apart from maintaining cell shape, involvement of PBP5 in maintaining intrinsic beta-lactam resistance is an important physiological observation and we speculate that such a strategy of deleting PBP5 may be helpful to introduce beta-lactam susceptibility in the laboratory.

A weak DD-carboxypeptidase activity explains the inability of PBP 6 to substitute for PBP 5 in maintaining normal cell shape in Escherichia coli

Penicillin-binding protein (PBP) 5 plays a critical role in maintaining normal cellular morphology in mutants of Escherichia coli lacking multiple PBPs. The most closely related homologue, PBP 6, is 65% identical to PBP 5, but is unable to substitute for PBP 5 in returning these mutants to their wild-type shape. The relevant differences between PBPs 5 and 6 are localized in a 20-amino acid stretch of domain I in these proteins, which includes the canonical KTG motif at the active site. We determined how these differences affected the enzymatic properties of PBPs 5 and 6 toward beta-lactam binding and the binding and hydrolysis of two peptide substrates. We also investigated the enzymatic properties of recombinant fusion proteins in which active site segments were swapped between PBPs 5 and 6. The results suggest that the in vivo physiological role of PBP 5 is distinguished from PBP 6 by the higher degree of DD-carboxypeptidase activity of the former.

Physiological functions of D-alanine carboxypeptidases in Escherichia coli

Bacterial cell shape is, in part, mediated by the peptidoglycan (murein) sacculus. Penicillin-binding proteins (PBPs) catalyze the final stages of murein biogenesis and are the targets of beta-lactam antibiotics. Several low molecular mass PBPs including PBP4, PBP5, PBP6 and DacD seem to possess DD-carboxypeptidase (DD-CPase) activity, but these proteins are dispensable for survival in laboratory culture. The physiological functions of DD-CPases in vivo are unresolved and it is unclear why bacteria retain these seemingly non-essential and enzymatically redundant enzymes. However, PBP5 clearly contributes to maintenance of cell shape in some PBP mutant backgrounds. In this review, we focus on recent findings concerning the physiological functions of the DD-CPases in vivo, identify gaps in the current knowledge of these proteins and suggest some possible courses for future study that might help reconcile current models of bacterial cell morphology.

Enantioselective synthesis of the antiinflammatory agent (-)-acanthoic acid

An enantioselective synthesis of the potent antiinflammatory agent (-)-acanthoic acid (1) is described. The successful strategy departs from (-)-Wieland-Miescher ketone (10), which is readily available in both enantiomeric forms and constitutes the starting point toward a fully functionalized AB ring system of 1. Conditions were developed for a regioselective double alkylation at the C4 center of the A ring, which produced compound 32 as a single stereoisomer. Construction of the C ring of 1 was accomplished via a Diels-Alder reaction between sulfur-containing diene 43 and methacrolein (36), which after desulfurization and further functionalization yielded synthetic acanthoic acid. The described synthesis confirms the proposed stereochemistry of the natural product and represents a fully stereocontrolled entry into an underexplored class of biologically active diterpenes.

Functioning oncocytic adenoma of the pituitary

A case of a functioning invasive pituitary oncocytoma in a 50-year-old man is reported. The serum prolactin was increased and immunocytochemical staining was positive for prolactin. In addition to numerous mitochondria within the neoplastic cells, structurally abnormal mitochondria with crystalline inclusions were also present. Another interesting feature was the presence of about 10 to 15% of non-oncocytic cells which showed prominent RER and Golgi apparatus as found in functioning pituitary adenomas. It is likely that these secretorily active cells were responsible for the functional activity of the tumour.

Medullomyoblastoma. A teratoma

Three cases of medullomyoblastoma in children are reported. The second case is unique in that in addition to areas of medulloblastoma and rhabdomyosarcoma, there were areas of well-differentiated teratoma containing all mature elements. This observation lends support to the teratomatous nature of medullomyoblastoma.

Neuroenteric cyst of the cerebellum

Intracranial neuroenteric cysts are rarely encountered and no more than 13 cases have been reported in the literature. This paper reports another case located in the cerebellum. These occur mostly in adults and there is no typical clinical presentation. The computed tomographic scan shows them as low attenuating lesions with no peripheral contrast enhancement. These cysts are believed to be developmental in origin.