New opportunities revealed by biotechnological explorations of extremophiles

Genomic mining of Geobacillus stearothermophilus GF16 for xylose production from hemicellulose-rich biomasses using secreted enzymes

The valorization of lignocellulosic biomass, derived from various bio-waste materials, has received considerable attention as a sustainable approach to improve production chains while reducing environmental impact. Microbial enzymes have emerged as key players in the degradation of polysaccharides, offering versatile applications in biotechnology and industry. Among these enzymes, glycoside hydrolases (GHs) play a central role. Xylanases, in particular, are used in a wide range of applications and are essential for the production of xylose, which can be fermented into bioethanol or find use in many other industries. Currently, fungal secretomes dominate as the main reservoir of lignocellulolytic enzymes, but thermophilic microorganisms offer notable advantages in terms of enzyme stability and production efficiency. Here we present the genomic characterization of Geobacillus stearothermophilus GF16 to identify genes encoding putative enzymes involved in lignocellulose degradation. Thermostable GHs secreted by G. stearothermophilus GF16 were investigated and found to be active on different natural polysaccharides and synthetic substrates, revealing an array of inducible GH activities. In particular, the concentrated secretome possesses significant thermostable xylanase and β-xylosidase activities (5 ×103 U/L and 1.7 ×105 U/L, respectively), highlighting its potential for application in biomass valorization. We assessed the hemicellulose hydrolysis capabilities of various agri-food wastes using the concentrated secretome of the strain cultivated on xylan. An impressive 300-fold increase in xylose release compared to a commercially available cocktail was obtained with the secretome, underscoring the remarkable efficacy of this approach.

An insight into the mechanisms of homeostasis in extremophiles

The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.

Thermostable lipases and their dynamics of improved enzymatic properties

Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed. KEY POINTS: • The dynamics of lipases contributes to their non-covalent interactions and structural stability. • Thermostability can be enhanced by well-established genetic tools for improved kinetic efficiency. • Molecular dynamics greatly provides structure-function insights on thermodynamics of lipase.

An Overview on Industrial and Medical Applications of Bio-Pigments Synthesized by Marine Bacteria

Marine bacterial species contribute to a significant part of the oceanic population, which substantially produces biologically effectual moieties having various medical and industrial applications. The use of marine-derived bacterial pigments displays a snowballing effect in recent times, being natural, environmentally safe, and health beneficial compounds. Although isolating marine bacteria is a strenuous task, these are still a compelling subject for researchers, due to their promising avenues for numerous applications. Marine-derived bacterial pigments serve as valuable products in the food, pharmaceutical, textile, and cosmetic industries due to their beneficial attributes, including anticancer, antimicrobial, antioxidant, and cytotoxic activities. Biodegradability and higher environmental compatibility further strengthen the use of marine bio-pigments over artificially acquired colored molecules. Besides that, hazardous effects associated with the consumption of synthetic colors further substantiated the use of marine dyes as color additives in industries as well. This review sheds light on marine bacterial sources of pigmented compounds along with their industrial applicability and therapeutic insights based on the data available in the literature. It also encompasses the need for introducing bacterial bio-pigments in global pigment industry, highlighting their future potential, aiming to contribute to the worldwide economy.

Improving the thermostability of a GH11 xylanase by directed evolution and rational design guided by B-factor analysis

Operational stability under high temperature is required for enzyme application in industrial processes. Error-prone PCR and B-factor analysis were employed to enhance the thermostability of a xylanase from GH family 11 in this study. Based on the top 10 mutants screened from the random mutation libraries, mutant Xyn371 was derived from the optimal mutant Xyn370 by integrating the beneficial residues identified in the other 9 screened mutants. Subsequently, a best-saturation mutant Xyn372 originated from Xyn371 was selected with a 60-min half-life at 70 °C (0.5-min half-life for the wild-type enzyme). According to the site-saturated mutagenesis of 10 residues with higher B-factors in Xyn372, mutants Xyn375 and Xyn376 were screened; their half-lives at 70 °C were 410 and 360 min, respectively. The substituted residues located in the "palm" region of the N-terminus and the newly generated hydrogen bonds in the mutants might contribute to improved thermostability. The significantly improved thermostability of mutants will pave the way for applications in different industrial areas.

Extremophile Microalgae: the potential for biotechnological application

Microalgae are photosynthetic microorganisms that use sunlight as an energy source, and convert water, carbon dioxide, and inorganic salts into algal biomass. The isolation and selection of microalgae, which allow one to obtain large amounts of biomass and valuable compounds, is a prerequisite for their successful industrial production. This work provides an overview of extremophile algae, where their ability to grow under harsh conditions and the corresponding accumulation of metabolites are addressed. Emphasis is placed on the high-value products of some prominent algae. Moreover, the most recent applications of these microorganisms and their potential exploitation in the context of astrobiology are taken into account.

The Aqueous Extract of Radio-Resistant Deinococcus actinosclerus BM2T Suppresses Lipopolysaccharide-Mediated Inflammation in RAW264.7 Cells

Deinococcus actinosclerus BM2^T (GenBank: KT448814) is a radio-resistant bacterium that is newly isolated from the soil of a rocky hillside in Seoul. As an extremophile, D. actinosclerus BM2^T may possess anti-inflammatory properties that may be beneficial to human health. In this study, we evaluated the anti-inflammatory effects of BM2U, an aqueous extract of D. actinosclerus BM2^T, on lipopolysaccharide (LPS)-mediated inflammatory responses in RAW264.7 macrophage cells. BM2U showed antioxidant capacity, as determined by the DPPH radical scavenging (IC₅₀ = 349.3 μg/ml) and ORAC (IC₅₀ = 50.24 μg/ml) assays. At 20 μg/ml, BM2U induced a significant increase in heme oxygenase-1 (HO-1) expression (p < 0.05). BM2U treatment (0.2-20 μg/ml) significantly suppressed LPS-induced increase in the mRNA expression of proinflammatory cytokines tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, and IL-6 (p < 0.05). BM2U treatment also suppressed the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2), which are involved in the production of inflammatory mediators. BM2U treatment also inhibited the activation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinases (MAPKs): JNK, ERK, and p-38 (p < 0.05). Collectively, BM2U exhibited anti-inflammatory potential that can be exploited in attenuating inflammatory responses.

Improving the Thermostability of Rhizopus chinensis Lipase Through Site-Directed Mutagenesis Based on B-Factor Analysis

In order to improve the thermostability of lipases derived from Rhizopus chinensis, we identified lipase (Lipr27RCL) mutagenesis sites that were associated with enhanced flexibility based upon B-factor analysis and multiple sequence alignment. We found that two mutated isoforms (Lipr27RCL-K64N and Lipr27RCL-K68T) exhibited enhanced thermostability and improved residual activity, with respective thermal activity retention values of 37.88% and 48.20% following a 2 h treatment at 50°C relative to wild type Lipr27RCL. In addition, these Lipr27RCL-K64N and Lipr27RCL-K68T isoforms exhibited 2.4- and 3.0-fold increases in enzymatic half-life following a 90 min incubation at 60°C. Together these results indicate that novel mutant lipases with enhanced thermostability useful for industrial applications can be predicted based upon B-factor analysis and constructed via site-directed mutagenesis.

Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists

Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.

Extremophile - An Adaptive Strategy for Extreme Conditions and Applications

The concurrence of microorganisms in niches that are hostile like extremes of temperature, pH, salt concentration and high pressure depends upon novel molecular mechanisms to enhance the stability of their proteins, nucleic acids, lipids and cell membranes. The structural, physiological and genomic features of extremophiles that make them capable of withstanding extremely selective environmental conditions are particularly fascinating. Highly stable enzymes exhibiting several industrial and biotechnological properties are being isolated and purified from these extremophiles. Successful gene cloning of the purified extremozymes in the mesophilic hosts has already been done. Various extremozymes such as amylase, lipase, xylanase, cellulase and protease from thermophiles, halothermophiles and psychrophiles are of industrial interests due to their enhanced stability at forbidding conditions. In this review, we made an attempt to point out the unique features of extremophiles, particularly thermophiles and psychrophiles, at the structural, genomic and proteomic levels, which allow for functionality at harsh conditions focusing on the temperature tolerance by them.

Alkaliphiles: The Versatile Tools in Biotechnology

The extreme environments within the biosphere are inhabited by organisms known as extremophiles. Lately, these organisms are attracting a great deal of interest from researchers and industrialists. The motive behind this attraction is mainly related to the desire for new and efficient products of biotechnological importance and human curiosity of understanding nature. Organisms living in common "human-friendly" environments have served humanity for a very long time, and this has led to exhaustion of the low-hanging "fruits," a phenomenon witnessed by the diminishing rate of new discoveries. For example, acquiring novel products such as drugs from the traditional sources has become difficult and expensive. Such challenges together with the basic research interest have brought the exploration of previously neglected or unknown groups of organisms. Extremophiles are among these groups which have been brought to focus and garnering a growing importance in biotechnology. In the last few decades, numerous extremophiles and their products have got their ways into industrial, agricultural, environmental, pharmaceutical, and other biotechnological applications.Alkaliphiles, organisms which thrive optimally at or above pH 9, are one of the most important classes of extremophiles. To flourish in their extreme habitats, alkaliphiles evolved impressive structural and functional adaptations. The high pH adaptation gave unique biocatalysts that are operationally stable at elevated pH and several other novel products with immense biotechnological application potential. Advances in the cultivation techniques, success in gene cloning and expression, metabolic engineering, metagenomics, and other related techniques are significantly contributing to expand the application horizon of these remarkable organisms of the 'bizarre' world. Studies have shown the enormous potential of alkaliphiles in numerous biotechnological applications. Although it seems just the beginning, some fantastic strides are already made in tapping this potential. This work tries to review some of the prominent applications of alkaliphiles by focusing such as on their enzymes, metabolites, exopolysaccharides, and biosurfactants. Moreover, the chapter strives to assesses the whole-cell applications of alkaliphiles including in biomining, food and feed supplementation, bioconstruction, microbial fuel cell, biofuel production, and bioremediation.

Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles

SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.

Enhancing control of cell-free metabolism through pH modulation

Engineering metabolism for the synthesis of bio-based products in non-model organisms can be challenging. One specific challenge is that biosynthetic pathways are often built from enzyme candidates sourced from diverse organisms, which can prove difficult to implement in recombinant hosts due to differences in their cellular environments (e.g. pH, cofactor balance). To address this problem, we report a cell-free synthetic biology approach for understanding metabolism in a range of environmental conditions, specifically under varied pH. The key idea is to control the pH of Escherichia coli-based cell-free systems for assessing pathway performance using enzymes sourced from organisms other than E. coli. As a model, we apply this approach to study the impact of pH on the n-butanol biosynthesis pathway derived from clostridia in E. coli lysates. Specifically, we exploit the open, cell-free reaction environment to explore pH outside the habitable range of E. coli, revealing insights into how chemical context impacts the interaction between native metabolism and heterologous enzymes. We find that the pH optimum for butanol production from acetyl-CoA is substantially lower than the optimal pH of glycolysis in E. coli-based crude lysates. In addition, pH is an essential factor to consider when activating metabolic pathways in the cell-free environment due to its effect on reaction yield or enzyme activity, the latter of which is demonstrated in this work for alcohol dehydrogenases from a range of extremophiles. Ultimately, altering metabolism through pH control will allow cell-free systems to be used in studying the metabolic state of organisms and identify suitable enzymes for pathway engineering.

Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India

Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.

Two new compounds from a marine-derived Streptomyces sp

Two new long-chain unsaturated compounds, (2E, 6E)-10-methoxy-3,7-dimethyl-10-oxodeca-2,6-dienoic acid (1) and (2E, 6E)-3,7,11-trimethyldodeca-2,6-dienedioic acid (2), together with seven known compounds were isolated from a marine-derived Streptomyces sp. Their structures were determined by spectroscopic methods, including 2D NMR techniques. Compounds 1 and 2 were investigated for their antibacterial activities.

Anandins A and B, Two Rare Steroidal Alkaloids from a Marine Streptomyces anandii H41-59

Anandins A (1) and B (2), two rare steroidal alkaloids, were isolated from the fermentative broth of a marine actinobacteria Streptomyces anandii H41-59. The gross structures of the two alkaloids were elucidated by spectroscopic methods including HR-ESI-MS, and NMR. Their absolute configurations were confirmed by single-crystal X-ray diffraction analysis and comparison of their experimental and calculated electronic circular dichroism spectra, respectively. Anandin A exhibited a moderate inhibitory effect against three human cancer cell lines MCF-7, SF-268, and NCI-H460 with IC₅₀ values of 7.5, 7.9, 7.8 μg/mL, respectively.

Calcium (II) - and dipicolinic acid mediated-biostimulation of oil-bioremediation under multiple stresses by heat, oil and heavy metals

The oil-producing Arabian Gulf states have hot summer seasons of about 7-month in length. Therefore, environmental oil spills should be bioremediated by the activity of indigenous, hydrocarbonoclastic (hydrocarbon-degrading) microorganisms with optimum growth at about 50 °C. Soils in such arid countries harbor thermophilic bacteria, whose oil-consumption potential is enhanced by calcium (II) - and dipicolinic acid (DPA)-supplement. Those organisms are, however, subjected to additional stresses including toxic effects of heavy metals that may be associated with the spilled oil. Our study highlighted the resistance of indigenous, thermophilic isolates to the heavy metals, mercury (II), cadmium (II), arsenic (II) and lead (II) at 50 °C. We also detected the uptake of heavy metals by 15 isolates at 50 °C, and identified the merA genes coding for Hg²⁺-resistance in 4 of the studied Hg²⁺-resistant isolates. Hg²⁺ was the most toxic metal and the metal toxicity was commonly higher in the presence of oil. The addition of Ca²⁺ and DPA enhanced the Hg²⁺-resistance among most of the isolates at 50 °C. Crude oil consumption at 50 °C by 4 selected isolates was inhibited by the tested heavy metals. However, Ca²⁺ and DPA limited this inhibition and enhanced oil-consumption, which exceeded by far the values in the control cultures.

Improving the thermostability of a fungal GH11 xylanase via site-directed mutagenesis guided by sequence and structural analysis

BACKGROUND

Xylanases have been widely employed in many industrial processes, and thermophilic xylanases are in great demand for meeting the high-temperature requirements of biotechnological treatments. In this work, we aim to improve the thermostability of XynCDBFV, a glycoside hydrolase (GH) family 11 xylanase from the ruminal fungus Neocallimastix patriciarum, by site-directed mutagenesis. We report favorable mutations at the C-terminus from B-factor comparison and multiple sequence alignment.

RESULTS

C-terminal residues 207-NGGA-210 in XynCDBFV were discovered to exhibit pronounced flexibility based on comparison of normalized B-factors. Multiple sequence alignment revealed that beneficial residues 207-SSGS-210 are highly conserved in GH11 xylanases. Thus, a recombinant xylanase, Xyn-MUT, was constructed by substituting three residues (N207S, G208S, A210S) at the C-terminus of XynCDBFV. Xyn-MUT exhibited higher thermostability than XynCDBFV at ≥70 °C. Xyn-MUT showed promising improvement in residual activity with a thermal retention of 14% compared to that of XynCDBFV after 1 h incubation at 80 °C; Xyn-MUT maintained around 50% of the maximal activity after incubation at 95 °C for 1 h. Kinetic measurements showed that the recombinant Xyn-MUT had greater kinetic efficiency than XynCDBFV (K_m, 0.22 and 0.59 µM, respectively). Catalytic efficiency values (k_cat/K_m) of Xyn-MUT also increased (1.64-fold) compared to that of XynCDBFV. Molecular dynamics simulations were performed to explore the improved catalytic efficiency and thermostability: (1) the substrate-binding cleft of Xyn-MUT prefers to open to a larger extent to allow substrate access to the active site residues, and (2) hydrogen bond pairs S208-N205 and S210-A55 in Xyn-MUT contribute significantly to the improved thermostability. In addition, three xylanases with single point mutations were tested, and temperature assays verified that the substituted residues S208 and S210 give rise to the improved thermostability.

CONCLUSIONS

This is the first report for GH11 recombinant with improved thermostability based on C-terminus replacement. The resulting Xyn-MUT will be an attractive candidate for industrial applications.

Rational synthetic combination genetic devices boosting high temperature ethanol fermentation

The growth and production of yeast in the industrial fermentation are seriously restrained by heat stress and exacerbated by heat induced oxidative stress. In this study, a novel synthetic biology approach was developed to globally boost the viability and production ability of S. cerevisiae at high temperature through rationally designing and combing heat shock protein (HSP) and superoxide dismutase (SOD) genetic devices to ultimately synergistically alleviate both heat stress and oxidative stress. HSP and SOD from extremophiles were constructed to be different genetic devices and they were preliminary screened by heat resistant experiments and anti-oxidative experiments, respectively. Then in order to customize and further improve thermotolerance of S. cerevisiae, the HSP genetic device and SOD genetic device were rationally combined. The results show the simply assemble of the same function genetic devices to solve heat stress or oxidative stress could not enhance the thermotolerance considerably. Only S. cerevisiae with the combination genetic device (FBA1p-sod-MB4-FBA1p-shsp-HB8) solving both stress showed 250% better thermotolerance than the control and displayed further 55% enhanced cell density compared with the strains with single FBA1p-sod-MB4 or FBA1p-shsp-HB8 at 42 °C. Then the most excellent combination genetic device was introduced into lab S. cerevisiae and industrial S. cerevisiae for ethanol fermentation. The ethanol yields of the two strains were increased by 20.6% and 26.3% compared with the control under high temperature, respectively. These results indicate synergistically defensing both heat stress and oxidative stress is absolutely necessary to enhance the thermotolerance and production of S. cerevisiae.

Microbial response to environmental stresses: from fundamental mechanisms to practical applications

Environmental stresses are usually active during the process of microbial fermentation and have significant influence on microbial physiology. Microorganisms have developed a series of strategies to resist environmental stresses. For instance, they maintain the integrity and fluidity of cell membranes by modulating their structure and composition, and the permeability and activities of transporters are adjusted to control nutrient transport and ion exchange. Certain transcription factors are activated to enhance gene expression, and specific signal transduction pathways are induced to adapt to environmental changes. Besides, microbial cells also have well-established repair mechanisms that protect their macromolecules against damages inflicted by environmental stresses. Oxidative, hyperosmotic, thermal, acid, and organic solvent stresses are significant in microbial fermentation. In this review, we summarize the modus operandi by which these stresses act on cellular components, as well as the corresponding resistance mechanisms developed by microorganisms. Then, we discuss the applications of these stress resistance mechanisms on the production of industrially important chemicals. Finally, we prospect the application of systems biology and synthetic biology in the identification of resistant mechanisms and improvement of metabolic robustness of microorganisms in environmental stresses.

Multifactorial level of extremostability of proteins: can they be exploited for protein engineering?

Research on extremostable proteins has seen immense growth in the past decade owing to their industrial importance. Basic research of attributes related to extreme-stability requires further exploration. Modern mechanistic approaches to engineer such proteins in vitro will have more impact in industrial biotechnology economy. Developing a priori knowledge about the mechanism behind extreme-stability will nurture better understanding of pathways leading to protein molecular evolution and folding. This review is a vivid compilation about all classes of extremostable proteins and the attributes that lead to myriad of adaptations divulged after an extensive study of 6495 articles belonging to extremostable proteins. Along with detailing on the rationale behind extreme-stability of proteins, emphasis has been put on modern approaches that have been utilized to render proteins extremostable by protein engineering. It was understood that each protein shows different approaches to extreme-stability governed by minute differences in their biophysical properties and the milieu in which they exist. Any general rule has not yet been drawn regarding adaptive mechanisms in extreme environments. This review was further instrumental to understand the drawback of the available 14 stabilizing mutation prediction algorithms. Thus, this review lays the foundation to further explore the biophysical pleiotropy of extreme-stable proteins to deduce a global prediction model for predicting the effect of mutations on protein stability.

Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating

The effect of microwave frequency electromagnetic fields on living microorganisms is an active and highly contested area of research. One of the major drawbacks to using mesophilic organisms to study microwave radiation effects is the unavoidable heating of the organism, which has limited the scale (<5 ml) and duration (<1 h) of experiments. However, the negative effects of heating a mesophile can be mitigated by employing thermophiles (organisms able to grow at temperatures of >60°C). This study identified changes in global gene expression profiles during the growth of Thermus scotoductus SA-01 at 65°C using dielectric (2.45 GHz, i.e., microwave) heating. RNA sequencing was performed on cultures at 8, 14, and 24 h after inoculation to determine the molecular mechanisms contributing to long-term cellular growth and survival under microwave heating conditions. Over the course of growth, genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. Genes involved in cell wall biogenesis and elongation were also upregulated, consistent with the distinct elongated cell morphology observed after 24 h using microwave heating. Analysis of the global differential gene expression data enabled the identification of molecular processes specific to the response of T. scotoductus SA-01 to dielectric heating during growth.

IMPORTANCE

The residual heating of living organisms in the microwave region of the electromagnetic spectrum has complicated the identification of radiation-only effects using microorganisms for 50 years. A majority of the previous experiments used either mature cells or short exposure times with low-energy high-frequency radiation. Using global differential gene expression data, we identified molecular processes unique to dielectric heating using Thermus scotoductus SA-01 cultured over 30 h in a commercial microwave digestor. Genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. These findings serve as a platform for future studies with mesophiles in order to better understand the response of microorganisms to microwave radiation.

Characterization of extracellular amylase produced by haloalkalophilic strain Kocuria sp. HJ014

The haloalkaliphilic bacterium Kocuria sp. (HJ014) has the ability to produce extracellular amylase. The aim of this study was to purify and characterize this protein. The amylase enzyme with a specific activity of 753,502 U/mg was purified 5.7- fold using Sepharose 4B and Sephacryl S-300 gel filtration columns. The molecular weight of the enzyme was 45,000 Da as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The amylase showed maximum activity at pH 9 and 50°C in the presence of 3.5 M NaCl. The Km was 3.0 mg/ml and Vmax 90.09 U/ml. It was found that extracellular amylase from Kocuria sp. has a high industrial potential.

Ergosterols from the Culture Broth of Marine Streptomyces anandii H41-59

An actinomycete strain, H41-59, isolated from sea sediment in a mangrove district, was identified as Streptomyces anandii on the basis of 16S rDNA gene sequence analysis as well as the investigation of its morphological, physiological and biochemical characteristics. Three new ergosterols, ananstreps A-C (1-3), along with ten known ones (4-13), were isolated from the culture broth of this strain. The gross structures of these new compounds were elucidated on the basis of extensive analysis of spectroscopic data, including HR-ESI-MS, and NMR. The cytotoxicities of these isolates against human breast adenocarcinoma cell line MCF-7, human glioblastoma cell line SF-268, and human lung cancer cell line NCI-H460 and their antibacterial activities in inhibiting the growth of Candida albicans and some other pathogenic microorganisms were tested. Compounds 3-8, 10 and 11 displayed cytotoxicity with IC50 values in a range from 13.0 to 27.8 μg/mL. However, all the tested compounds showed no activity on C. albicans and other bacteria at the test concentration of 1 mg/mL with the paper disc diffusion method.

Extremophiles and biotechnology: current uses and prospects

Biotechnology has almost unlimited potential to change our lives in very exciting ways. Many of the chemical reactions that produce these products can be fully optimized by performing them at extremes of temperature, pressure, salinity, and pH for efficient and cost-effective outcomes. Fortunately, there are many organisms (extremophiles) that thrive in extreme environments found in nature and offer an excellent source of replacement enzymes in lieu of mesophilic ones currently used in these processes. In this review, I discuss the current uses and some potential new applications of extremophiles and their products, including enzymes, in biotechnology.

Enhancing stress-resistance for efficient microbial biotransformations by synthetic biology

Chemical conversions mediated by microorganisms, otherwise known as microbial biotransformations, are playing an increasingly important role within the biotechnology industry. Unfortunately, the growth and production of microorganisms are often hampered by a number of stressful conditions emanating from environment fluctuations and/or metabolic imbalances such as high temperature, high salt condition, strongly acidic solution, and presence of toxic metabolites. Therefore, exploring methods to improve the stress tolerance of host organisms could significantly improve the biotransformation process. With the help of synthetic biology, it is now becoming feasible to implement strategies to improve the stress-resistance of the existing hosts. This review summarizes synthetic biology efforts to enhance the efficiency of biotransformations by improving the robustness of microbes. Particular attention will be given to strategies at the cellular and the microbial community levels.

Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species

Background

The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures.

Results

The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified.

Conclusions

The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.

Purification and characterization of a cold-adapted lipase from Oceanobacillus strain PT-11

We isolated a moderately halophilic lipase-producing bacterium from the saline soil. Based on the morphological, physiological, chemotaxonomic and phylogenetic analysis, the isolate PT-11 was postulated to be a novel species identified as Oceanobacillus rekensis PT-11. The lipase was purified 2.50-fold by Q-Sepharose FF and SP-Sepharose FF chromatography and its molecular mass was estimated to be 23.5 kDa by SDS-PAGE. It was highly active over the broad temperature ranging from 10 to 35°C and showed up to 80% of the maximum activity at 10°C indicating the lipase to be a typical cold-adapted enzyme. The enzyme activity was slightly enhanced by Na+, Li+ and K+. Incubation with detergents, such as Tween-20 and Tween-80, slightly inhibited the enzyme activity; while Triton X-100decreased the enzyme activity. The enzyme was fairly stable in the presence of long-chain alcohols but was highly denatured in hydrophilic solvents such as acetone or short-chain alcohols (C1-C3).

Screening for genes coding for putative antitumor compounds, antimicrobial and enzymatic activities from haloalkalitolerant and haloalkaliphilic bacteria strains of Algerian Sahara Soils

Extreme environments may often contain unusual bacterial groups whose physiology is distinct from those of normal environments. To satisfy the need for new bioactive pharmaceuticals compounds and enzymes, we report here the isolation of novel bacteria from an extreme environment. Thirteen selected haloalkalitolerant and haloalkaliphilic bacteria were isolated from Algerian Sahara Desert soils. These isolates were screened for the presence of genes coding for putative antitumor compounds using PCR based methods. Enzymatic, antibacterial, and antifungal activities were determined by using cultural dependant methods. Several of these isolates are typical of desert and alkaline saline soils, but, in addition, we report for the first time the presence of a potential new member of the genus Nocardia with particular activity against the yeast Saccharomyces cerevisiae. In addition to their haloalkali character, the presence of genes coding for putative antitumor compounds, combined with the antimicrobial activity against a broad range of indicator strains and their enzymatic potential, makes them suitable for biotechnology applications.

A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1

Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99 Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium-proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes.

Engineering cellular robustness of microbes by introducing the GroESL chaperonins from extremophilic bacteria

The cellular robustness is a big concern for efficient microbial production of biofuels and biochemicals. In this study, the groESL genes from extremophilic bacteria were found to serve as transplantable stress-response elements to improve diverse types of stress-tolerances of other microbes. By overexpressing the groESL from the solvent-tolerant Pseudomonas putida in Escherichia coli, its thermo-tolerance and ethanol-tolerance were significantly increased. Meanwhile, the groESL from the thermophilic Thermoanaerobacter tengcongensis endowed Clostridium acetobutylicum with improved corn cob hydrolysates (CCH)-tolerance as well as elevated butanol productivity. The chaperonins GroESL have been widely considered as cellular stress-response proteins and overexpression of native groESL has been proven to improve cellular tolerances facing various stresses. Here we found that the groESL genes from extremophilic bacteria were superior to the native ones, possibly because they have adapted to the environmental stresses during long-term natural evolution. Moreover, our results also revealed that different extreme groESL genes performed quite different in different microbes. Thus the relation and compatibility between the extremophiles and the host must be considered for selection of the proper groESL for engineering microbial robustness.

Isolation and phylogenic identification of soil haloalkaliphilic strains in the former Texcoco Lake

A wide diversity of organisms exists in soil. Well-adapted groups can be found in extreme environments. A great economic and metabolic potential for extremozymes produced by organisms living at extreme environments has been reported. Extreme characteristics such as high salt content and high pH level make the soil of the former Texcoco Lake a unique place which has not been exploited. Therefore, in this study, 66 strains from soil of the former Texcoco Lake were isolated and phylogenetically analyzed using universal oligonucleotide primers. Different genera such as Kocuria, Micrococcus, Nesterenkonia, Halomonas, Salinicoccus, Kurthia, Gracilibacillus, and Bacillus were found. However, only 22 from all isolated strains were identified at specie level.

Paenibacillus marinum sp. nov., a thermophilic xylanolytic bacterium isolated from a marine hot spring in Tunisia

Among a large collection of Tunisian hot springs bacterial isolates a bacterial strain, THE22(T) , with xylanolytic properties was identified. The bacterium was isolated from a natural hot spring "Ain Echefa" at Mediteranean sea (Korbous, North-Eastern Tunisia). The novel strain was Gram positive, spore-forming, rod-shaped, facultatively anaerobic and grew optimally under conditions of 55 °C, 1% (w/v) NaCl and pH 7-8. The 16S rRNA gene sequence analysis showed that strain THE22(T) fell within the radiation of the cluster comprising Paenibacillus species with Paenibacillus phyllosphaerae PALXIL04(T) as the closest phylogenetic neighbour (95.8%). The predominant components in the fatty methyl ester profile were iso-C16:0 (34.46%), C16:0 (19.64%), anteiso-C15:0 (19.18%) and anteiso-C17:0 (18.11%). The major respiratory quinone was menaquinone-7 (MK-7). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The base composition of DNA was 56 mol%. Based on the polyphasic taxonomic data, strain THE-22(T) (=DSM 18499(T) = LMG 23758(T) ) was recognized as a novel species within the genus Paenibacillus. The name Paenibacillus marinum sp. nov. is proposed.

Biotechnological potential and conservatory of extremophiles from climatically wide ranged developing countries: Lesson from Pakistan

Abstract Technological advances, in developing countries, without considering environmental health issues have generated microsites uninhabitable to organisms including usual bacteria. While extremophilic microorganisms thrive in such locations. It is the high time to isolate and conserve the extremophilic biodiversity from such man made habitats before the environmental awareness treats them to the level of "destructionâ. For biotechnology processes to be geared by employing extremophilic microorganisms, locations characterized with high/low temperature for most part of the year, hypersaline brine and abneutral pH environments may render the respective microbes to do their allotted/required jobs with minimal of extraneous investments. Besides, many known and expected potentials of extremophilic bacteria for biotechnological applications, major attraction lies in operating bioprocesses under non-aseptic conditions for making them economically feasible. This review after giving a thumbnail picture of extremophilies' known features is centered on the triad of biodiversity richness, environmental availabilities/managements of locations suitable for respective biotechnological bioprocesses and their non-aseptic designing for a developing country like Pakistan.