Background: Virtually all eukaryotic cells contain spatially distinct genomes, a single nuclear genome that harbours the vast majority of genes and much smaller genomes found in mitochondria present at thousands of copies per cell. To generate a coordinated gene response to various environmental cues, the genomes must communicate with each another. Much of this bi-directional crosstalk relies on epigenetic processes, including DNA, RNA, and histone modification pathways. Crucially, these pathways, in turn depend on many metabolites generated in specific pools throughout the cell, including the mitochondria. They also involve the transport of metabolites as well as the enzymes that catalyse these modifications between nuclear and mitochondrial genomes. Scope of review: This study examines some of the molecular mechanisms by which metabolites influence the activity of epigenetic enzymes, ultimately affecting gene regulation in response to metabolic cues. We particularly focus on the subcellular localisation of metabolite pools and the crosstalk between mitochondrial and nuclear proteins and RNAs. We consider aspects of mitochondrial-nuclear communication involving histone proteins, and potentially their epigenetic marks, and discuss how nuclear-encoded enzymes regulate mitochondrial function through epitranscriptomic pathways involving various classes of RNA molecules within mitochondria. Major conclusions: Epigenetic communication between nuclear and mitochondrial genomes occurs at multiple levels, ultimately ensuring a coordinated gene expression response between different genetic environments. Metabolic changes stimulated, for example, by environmental factors, such as diet or physical activity, alter the relative abundances of various metabolites, thereby directly affecting the epigenetic machinery. These pathways, coupled to regulated protein and RNA transport mechanisms, underpin the coordinated gene expression response. Their overall importance to the fitness of a cell is highlighted by the identification of many mutations in the pathways we discuss that have been linked to human disease including cancer.

Introduction

To fit within the confined space of a eukaryotic nucleus, a cell’s genome must be efficiently compacted, but in a highly ordered manner that maintains accessibility to the genetic information. This is achieved by DNA complexing with histone proteins to form nucleosome structures, which in turn further compact to form chromatin that ultimately packages entire chromosomes. Importantly, chromatin is not an inert packaging structure but rather an instructive scaffold capable of responding to various cues to regulate access of the DNA to different cellular machineries. This accessibility is fundamentally regulated by ATP-dependent chromatin remodelling activities and by covalent modification of both DNA and histone proteins. These modifications are commonly referred to as “epigenetic” modifications. Furthermore, in addition to epigenetics, the emerging field of epitranscriptomics is now adding numerous modifications of RNA molecules to the “modification repertoire,” thereby expanding our current view of epigenetics and how it regulates all DNA processes, in particular gene expression [1]. DNA and histone modifications regulate gene expression by modulating chromatin accessibility and/or providing binding sites for regulatory proteins. To date, more than 100 post-translational modifications (PTMs) have been detected on histones, including acetylation, methylation, ubiquitylation, phosphorylation, citrullination, and O-GlcNAcylation. Of these, acetylation and methylation are by far the best-studied and most characterised histone modifications (for review, see [2,3]).

Basics Considerations on Enzymes

Enzymes have been used for millennia in food processing, such as bread baking, brewing, cheese and wine making, although only in the later decades of the 20th century, processes were developed that allowed the production in well-characterized formulations, even at large scale (Kirk et al., 2002; Mishra et al., 2017). Enzymes are globular proteins that act as catalysts, thus they speed up the rate of a reaction by lowering the energy of activation. Some enzymes require cofactors, small organic molecules or metal ions, for catalytic activity. Unlike chemical catalysts, enzymes are natural in origin, operate under mild temperature and pressure, display high specificity and are biodegradable (van Oort, 2010; Subin and Bhat, 2015). Biologically active enzymes can be obtained from animals, microorganisms and plants, but microbial sources are favored. Microbial enzymes can be produced in high yield, in relatively low-cost and short time processes, and are typically more stable than enzymes from the remaining sources. Particularly preferred are microbial produced enzymes that are secreted to the fermentation medium, as this eases separation and purification. Genetically modified microorganisms expressing exogenous enzymes (from plant or animal sources and from pathogenic or difficult to grow microbial strains) are also used in commercial enzyme production (Chandrasekaran et al., 2015; Subin and Bhat, 2015). Enzyme activity and stability are influenced by operational conditions, e.g., pH, temperature, substrate concentration, presence of metal ions and enzyme concentration. Enzymes have optimal pH and temperature conditions for activity and stability that may not fully match in an industrial process. An increase in substrate concentration increases activity up to a given point, henceforth the rate of reaction stabilizes or may even decrease, in case of substrate inhibition. Also depending on the enzyme, given metal ions may be required for activity (e.g., Ca2þ for most a-amylases), or may inhibit enzyme activity (Subin and Bhat, 2015). Thus, careful selection of operating conditions is critical for high enzyme performance. This is relatively easy to implement in laboratory condition with model systems, but may prove difficult to reproduce with real systems, due to the complexity of the matrix to be processed, e.g., hydrolysis of lactose in buffer system or industrial scale hydrolysis of lactose in milk. Enzymes can be used in free form or immobilized, e.g., attached to/entrapped in an inert support, to allow the repeated/continuous use of the enzyme, and to also increase its stability. Still, the implementation of an immobilized enzyme based system at industrial scale requires a careful evaluation as in addition to technical issues, e.g., loss of activity during immobilization, mass transfer limitations, the economics of immobilized enzymes, e.g., cost of immobilization, cost of immobilization carrier and chemicals for immobilization, must be considered (DiCosimo et al., 2013; Sheldon and van Pelt, 2013).

The enzyme catalase is known to catalyse the breakdown of hydrogen peroxide into oxygen and water. Hydrogen peroxide metabolism is mainly regulated by this enzyme. Catalase is a common enzyme found in nearly all living organisms. It has one of the highest turnovers of all enzymes as it has the capacity to decompose more than one million molecules of hydrogen peroxide, per molecule of enzyme. Catalase has been used as an important enzyme in many biotechnological areas including bioremediation. This paper gives a review of its use and application in the field of bioremediation as an indicator of hydrocarbon degradation in soil (an important aspect in bioremediation of crude oil pollution), as a provider of oxygen in aerobic bioremediation process and in the removal of H2O2 from bleaching industry effluent and also its potential use in the food industry.

Introduction

Catalase (EC 1.11.1.6) enzyme is an oxidoreductase enzyme as it plays a crucial role in quenching the reactive oxygen species (ROS), i.e. hydrogen peroxide, often produced as a by-product of aerobic respiration (Beers and Sizer., 1952). Hence it acts as an antioxidant and protects the cell against oxidative stress (Abbott et al., 2009, Kirkman et al., 1987). The enzyme is found in a wide range of aerobic and anaerobic organisms. Catalase has one of the highest turnover number as one molecule of enzyme hydrolysing over a million molecules of the substrate i.e. hydrogen peroxide per second. New applications for catalases are constantly emerging thanks to their high turnover number (Lončar and Fraaije 2015, Zamocky et al., 1999), distinct evolutionary origin, reasonably simple (Alptekin et al. 2008) and well-defined reaction mechanisms (Baeza et al., 2013). The basic mechanism of the working of this enzyme involves the breakdown and subsequent breakdown of the reactive oxygen specie i.e. hydrogen peroxide (H2O2) into oxygen and water thus relieving the oxidative stress caused by this substrate as depicted in the following reaction (Barynin et al., 2001). Catalase is a tetramer of four polypeptide chains, each over 500 amino acids long. It contains four porphyrin heme (iron) groups that allow the enzyme to react with the hydrogen peroxide. Catalase has a fairly broad range of working from 4-11 optimum pH (Beers, 1961; Calera et al., 2000; Correia et al., 1994; Diaz et al., 2012). Catalase is usually located in a cellular, bipolar environment organelle called the peroxisome (Fita et al., 1985). As this enzyme is found in mainly all organisms (aerobic and anaerobic), it has been exploited in many applications including food processing, textile, paper, pharmaceutical industry and also in the field of bioremediation as one of the upcoming areas of its application (Gromada et al., 1997; Hussein 2012; . Beers et al., 1952; Youn et al 1995).This paper intends to give an account of how this enzyme has been exploited in the process of bioremediation in order to clean the environment of unwanted substances.

Terrestrial ecosystems represent a major sink of CO2 through fixation by plants but they have been shown to mitigate the rise of atmospheric CO2 also via microbial CO2 fixation (Ge et al., 2016; Yuan et al., 2012). Microbial CO2 fixation has been mostly ascribed to autotrophic microorganisms (Ge et al., 2016), but fundamentally all microorganisms may use inorganic C (IC; i.e. CO2 or bicarbonate) in their metabolism. All these fixations require energy generated by phototrophic, autotrophic or heterotrophic energy sources. IC is the main or even the only C source for chemoautotrophs and photoautotrophs, while heterotrophs and mixotrophs rely on organic C (OC) but also incorporate IC via a variety of carboxylation reactions that are part of their central or peripheral metabolic pathways (for review see Erb, 2011; Wood and Stjernholm, 1962). The importance of carboxylases in heterotrophic metabolism increases whenever microorganisms experience C limitation through a disproportion between C demand for energy generation and growth and its availability, caused by deficiency or complexity of OC sources, or fast growth (Alonso-Saez et al., 2010; Feisthauer et al., 2008; Merlin et al., 2003). Even though the occurrence of dark and largely heterotrophic CO2 fixation in soils is generally accepted, very few studies have assessed its relevance for soil microorganisms (Miltner et al., 2004, 2005a,b; Šantrůčková et al., 2005). Estimates of the importance of soil CO2 fixation for the C balance in certain ecosystems or within an entire soil profile are rare (Ge et al., 2016; Yuan et al., 2012) and analyses of diversity and abundance of carboxylases are missing entirely. Soil OC becomes progressively enriched in 13C with increasing soil depth (Bird et al., 2002; Gentsch et al., 2015; Nadelhoffer and Fry, 1988; Torn et al., 2002). There are several explanations but no one can fully explain the measured isotopic shift. The enrichment of soil OC with depth can be connected with decrease of δ 13C of atmospheric CO2 by 1.3‰ due to Suess effect (McCarroll and Loader, 2004), with preferential decomposition of different organic compounds and microbial fractionation during litter decomposition or mixing of new C input with old soil OC (Buchmann et al., 1997; Ehleringer et al., 2000; Šantrůčková et al., 2000). Another hypothesis that has been discussed but never supported experimentally states that soil microbes should be isotopically heavier as a result of carboxylation reactions (Ehleringer et al., 2000). Whenever carboxylation reactions are involved, CO2 molecules used in the reactions likely originate from the soil atmosphere, which is isotopically heavier than the organic materials being decomposed (Cerling et al., 1991). The 13CO2 enrichment of bulk soil atmosphere is highest in the uppermost soil horizons, where CO2 originates mostly from the atmospheric air. In deeper horizons of the soil profile, CO2 originates from organic matter decomposition and carries the isotopic signal of decomposed material. But still CO2 remaining in the soil that surrounds microbes is 4.4‰ heavier than organic matter at the location due to slower diffusion of heavier 13CO2 than lighter 12CO2 (Cerling et al., 1991). CO2 hydrogenation causes further enrichment of 13C in HCO3 − by 8–12‰, depending on temperature (Mook et al., 1974).

There is an increasing concern about pathogenic bacteria obtaining resistance to the antibiotics used for treatment of humans and animals. To address the problems with antibiotic resistance we need knowledge about the various resistance mechanisms, how they can be disseminated, which bacteria contain them and where they come from. Antibiotic resistance is not a new phenomenon, see e.g. review by [1]. There are many ways bacteria can obtain and exert antibiotic resistance and new resistance determinants are continuously discovered. The strategies bacteria use to evade the effects of antibiotics, can be grouped into three general mechanisms: increased antibiotic efflux out of the cell or reduced antibiotic influx into the cell, enzymatic inactivation of antibiotics through drug modification or cleavage, and the alteration of the antibiotic binding site. A bacterial cell contains many different target sites for antibiotics, but in general, an antibiotic interfere with or inhibits an essential cellular pathway or process. The most common antibiotic targets include bacterial cell wall synthesis; the bacterial membrane; the DNA replication machinery; RNA polymerase; the folate biosynthesis pathway; and the protein synthesis machinery. The ribosome is a major site of antibiotic action in the bacterial cell and is targeted by a large and chemically diverse group of antibiotics. A number of these antibiotics have important applications in human and veterinary medicine in the treatment of bacterial infections. The antibiotic binding sites are clustered at functional centers of the ribosome, such as the decoding center on the 30S subunit, the peptidyl transferase center (PTC), the GTPase center, and the peptide exit tunnel on the 50S subunit and the subunit interface in the 70S ribosome. The resistance mechanisms to antibiotics targeting the ribosomes include all three mechanism mentioned above. The alterations of the ribosomal antibiotic binding sites providing antibiotic resistance can be either mutation or methylation. While mutations appear spontaneously the gaining of methylations normally need a gene transfer of a methyl transferase gene. Since the 1950s, about 17 methyltransferases providing antibiotic resistance has been discovered, reviewed by [2,3]. One of the most recently discovered and most exceptional regarding nature of modification and mechanism of methylation is the Cfr methyltransferase [4e7] and Cfr and Cfr-like proteins have a potential to become a serious threat for antibiotic treatment. The sections below will present an overview of our current knowledge about Cfr and Cfr-like methyltransferases and especially cover aspects that have not previously been reviewed.

هدف از این مطالعه بررسی اثرات 1) افشانه سلول های خونی خشک شده غنی از هیستیدین و 2) تاثیر هیستیدین خالص اضافه شده به غذ ا در وضعیت آنتی اکسیدانی و غلظت مولکول های مرتبط با کارنوزین در خون و گوشت سینه بوقلمون های ماده ، می باشد . آزمايش بر روي 168 بوقلمون ماده بیگ 7 صورت گرفت . سه رژیم غذایی به طور تصادفی برای بوقلمون های مورد بررسی اعمال شد: رژیم غذایی کنترل ؛ رژیم غذایی کنترل بعلاوه 0.18٪ L-هیستیدین (His)؛ و رژیم غذایی کنترل بعلاوه افشانه گلبول های قرمز خون خشک شده( SDBC). . پرنده ها برای مدت 103 روز در بستری با خاک اره، آب آشامیدنی و تغذیه اختیاری (تغذیه با خوراک نامحدود دام) نگهداری شدند. وضعیت آنتی اکسیدانی پلاسمای خون و عضله سینه با توانایی کاهش آهن (FRAP) و توانایی جمع آوری رادیکال ها توسط 2,2-Azinobis-(3- ethylbenzothiazoline-6-sulfonic acid) (ABTS) و 1,1- Diphenyl-2-picrylhydrazyl (DPPH) مورد ارزیابی قرار گرفت. فعالیت آنزیم های آنتی اکسیدانی سوپر اکسید دیسموتاز (SOD)، کاتالاز (CAT) و گلوتاتیون پراکسیداز (GPx) در خون و گوشت سینه با محتوای آنزیم و کارنوزین با استفاده از HPLC اندازه گیری شد. آنالیز تقریبی و همچنین آنالیز آمینو اسید برای خوراک و عضلات سینه انجام شد .

جمع آوری خون و آماده سازی عضلات برای آنالیز
نمونه های خون در طی کشتار جمع آوری و سپس بلافاصله هپارینیزه شدند، روی یخ قرار داده شدند و برای جداسازی پلاسما از سلول های خونی سانتریفیوژ ( 5,000 G) شدند. فعالیت GPx، و همچنین ظرفیت آنتی اکسیدان 2,2-Azinobis-(3 ethylbenzothiazoline-6- sulfonic acid) (ABTS); 1,1-Diphenyl-2-picrylhydrazyl (DPPH); توانایی کاهش آهن (FRAP) در پلاسما تعیین شد. رسوب سلول های خونی برای بررسی فعالیت CAT پس از 3 بار شستشو با محلول سرد 0.15 میلی گرم NaCl مورد استفاده قرار گرفت و در G 5,000. سانتریفیوژ شد.

مقاله سال 2016

تاثیرات مصرف دانه و مکمل آنزیم کربوهیدرات در فیزیولوژی گوارش مرغ مورد بررسی قرار گرفت. مجموع 625 عدد جوجه یک روزه (راس 308) به طور تصادفی با پنج روش تیمار مختلف در طرحی کاملا تصادفی قرار گرفتند. تیمار ، شامل دو نوع مختلف از دانه ها (گندم و جو) می شد که با مکمل یا بدون مکمل کربوهیدرات چندگانه بود. رژیم ذرت نیز مطرح شده تا به عنوان یک تنظیم کننده بکار رود. مصرف خوراک جو با مکمل کربوهیدرات چندگانه منجر به جذب بیشتر خوراک (P <0.01) نسبت به آن دسته که از رژیم های غذایی ذرت و گندم در تغذیه شان استفاده کرده بودند می شود . پرندگانی که از رژیم غذایی جو و گندم تغذیه کردند افزایش وزن کمتری داشتند با وجود اینکه میزان جذب بالاتری در خوراک داشتند (P <0.01).تعداد کل و شمار مختلفی از باکتری ها از جمله گرم منفی، اشریشیا کلی، و کلستریدیا پس از تغذیه گندم و جو کاهش یافت اما تعداد لاکتوباسیل و بیفیدوباکتریوم افزایش یافت (P <0.01). تغذیه رژیم جو و گندم ارتفاع پرزها در قسمت های مختلف روده کوچک را در مقایسه با آنهایی که از رژیم ذرت تغذیه کردند کاهش می دهد.با این حال ، مکمل آنزیمی جو و رژیم غذایی گندم وزن مفید و میزان جذب غذا را افزایش داده و در نتیجه تعداد باکتری E. coli و کلستریدیا کاهش داده و تعداد لاکتوباسیل ها و بیفیدوباکتریوم را افزایش می دهد ، و همچنین اثرات منفی بر روی ارتفاع پرزهای روده (P <0.01) را ترمیم می کند. فعالیت های پانکراس α-آمیلاز و لیپاز (P <0.01) در جوجه هایی که خوراک گندم و رژیم های غذایی جو داشتند در مقایسه با تغذیه اصلاح شده رژیم غذایی ذرت افزایش یافته بود .مکمل آنزیمی فعالیت های پانکراس α-آمیلاز و لیپاز (P <0.01) را کاهش می دهد. در نتیجه، رژیم های غذایی مختلف بدون نشاسته پلی ساکاریدی که فاقد مکمل آنزیمی هستند ، تاثیر سوء بر گرانروی مواد هضمی ، فلور روده، مورفولوژی پرز و فعالیت آنزیم پانکراس می گذارند.