Enzyme Genomics

Veronese G (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 20( 11) 1605—1612 Taylor M, Marmer W, Brown E (2007) Evaluation of polymers prepared from gelatin and casein or whey as potential fillers. J Am Leather Chem Assoc 102(4) 111-120... 

Taherzadeh, M.J., Karimi, K., 2007. Enzymatic-based hydrolysis processes for ethanol. BioResources 2 (4), 707-738. Tasse, L., Bercovici, J., Pizzut-Serin, S., Robe, R, Tap, J., Klopp, C., Cantarel, B.L., et al., 2010. Fvmctional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Research 20 (11), 1605-1612. Van Berkel, R., 2000. Cleaner Rroduction for Rrocess Industries. Plenary Lecture. Chemeca, Perth WA. 

The genome, through its constituent DNAs, provides all of the codes needed for building a wide range of peptides, proteins, and enzymes, which in turn utilize raw materials (food) to form an animate body and keep it going. These multiple reactions work together as a unit within a water-filled cell. 

Biochemistry resulted from the early elucidation of the pathway of enzymatic conversion of glucose to ethanol by yeasts and its relation to carbohydrate metaboHsm in animals. The word enzyme means "in yeast," and the earfler word ferment has an obvious connection. Partly because of the importance of wine and related products and partly because yeasts are relatively easily studied, yeasts and fermentation were important in early scientific development and stiU figure widely in studies of biochemical mechanisms, genetic control, cell characteristics, etc. Fermentation yeast was the first eukaryote to have its genome elucidated. 

Wn, R., 1993. Development of enzyme-ba.sed mediods for DNA. sequence analy.sis and dieir application in genome projects. Methods in Enzymology 67 431-468. 

The space inside the inner mitochondrial membrane is called the matrix, and it contains most of the enzymes of the TCA cycle and fatty acid oxidation. (An important exception, succinate dehydrogenase of the TCA cycle, is located in the inner membrane itself.) In addition, mitochondria contain circular DNA molecules, along with ribosomes and the enzymes required to synthesize proteins coded within the mitochondrial genome. Although some of the mitochondrial proteins are made this way, most are encoded by nuclear DNA and synthesized by cytosolic ribosomes. 

For the CTX-M family which has been rapidly growing during the last three years genomic data have identified the genome of Kluyvera species as the genetic source of progenitor enzymes (e.g. encoding CTX-Ml, CTX-M2 or CTX-M9). 

Viruses are small infectious agents composed of a nucleic acid genome (DNA or RNA) encased by structural proteins and in some cases a lipid envelope. They are the causative agents of a number of human infectious diseases, the most important for public health today being acquired immunodeficiency syndrome (AIDS), hepatitis, influenza, measles, and vituses causing diarrhoea (e.g., rotavirus). In addition, certain viruses contribute to the development of cancer. Antiviral drugs inhibit viral replication by specifically targeting viral enzymes or functions and are used to treat specific virus-associated diseases. 

Another type of NR crosstalk, which has only recently been recognized, is the so-called nongenomic actions of several receptors that induce very rapid cellular effects. Effectively, evidence has accumulated over several decades that steroid receptors may have a role that does not require their transcriptional activation, such as modifying the activity of enzymes and ion channels. While the effects of steroids that are mediated by the modulation of gene expression do occur with a time lag of hours, steroids can induce an increase in several second messengers such as inositol triphosphate, cAMP, Ca2+, and the activation of MARK and PI3 kinase within seconds or minutes. Many mechanistic details of these nongenomic phenomena remain poorly understood. Notably, controversy still exists as to the identity of the receptors that initiate the non-genomic steroid actions. However, it now appears that at least some of the reported effects can be attributed to the same steroid receptors that are known as NRs. 

Burroughs AM, Allen KN, Dunaway-Mariano D et al (2006) Evolutionary genomics of the HAD superfamily understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol 361 1003-1034... 

Reverse transcription is the copying of an RNA molecule back into its DNA complement. The enzymes that perform this function are called reverse transcriptases. Reverse transcription is used naturally by retroviruses to insert themselves into an organism s genome. Artificially induced reverse transcription is a useful technique for translating unstable messenger RNA (mRNA) molecules into stable cDNA. 

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