78 Matching Annotations
  1. Nov 2018
    1. P. Kersey et al., Nucleic Acids Res. 33, D297–D302 (2005).

      This paper presents intrgr8. Intrgr8 is a database that helps researchers find information about the many different genomes that have been sequenced. Specifically, it links the sequenced genomes to information about that organism's proteins and any papers published about the genome.

    2. 12. C. M. Silva et al., J. Polym. Sci. A Polym. Chem. 43, 2448–2450 (2005).

      Describes the use of a cutinase from Fusarium solani pisi to degrade the surfaces of fibers to make them more hydrophilic and appropriate for use in the clothing industry. They found that the cutinase degraded the surface of a variety of fibers, including PET, to varying extents.

    3. 2. R. J. Müller, I. Kleeberg, W. D. Deckwer, J. Biotechnol. 86, 87–95 (2001).

      In this review, the authors discuss the work to create polymers that are both biodegradable and useful. Historically, most aliphatic polymers did not have the correct properties to be useful and most aromatic polymers were difficult to biodegrade. The review article details different techniques for making copolymers which have portions that are aromatic and portions that are aliphatic, allowing them to be both biodegradable and useful.

    4. However, among the 92 microorganisms with MHETase homolog(s), 33 had homologs of both TPA and PCA dioxygenases. This suggests that a genomic basis to support the metabolism of MHET analogs was established much earlier than when ancestral PETase proteins were incorporated into the pathway. PET enrichment in the sampling site and the enrichment culture potentially promoted the selection of a bacterium that might have obtained the necessary

      The authors looked for other organisms that might have similar DNA coding for enzymes that can degrade PET. However, despite finding several organisms with the metabolism needed to degrade MHET, they were unable to find any with PETase enzymes.

      The authors concluded that the enzymes needed to degrade MHET predate PETase enzymes. They hypothesize that the PETase may have evolved from the similar enzyme family cutinase and then been passed from bacterium to bacterium in the PET-rich recycling site.

      Since the recycling site where the authors took their original samples had a lot of PET, bacteria with the ability to degrade PET may have been more able to survive and divide. This would have encouraged the spread of the PETase genes in the recycling site l. sakaiensis population.

    5. The catalytic triad residues and two cysteine residues found only in this family

      In 2014, Suzuki et al. discovered a new structure in proteins featuring five specific amino acids held closely together.

      The structure begins with an amino acid called serine somewhere on a protein next to an amino acid called cysteine. They link to another cysteine next to an amino acid called histidine in such a way that a fifth amino acid, called aspartic acid and located between the two pairs is held closely to them in 3D space.

    6. maltose

      Maltose is a disaccharide sugar that is closely related to sucrose (table sugar). Sucrose is made of two simple sugars—glucose and fructose—whereas maltose is made of two glucose molecules.

    7. mesophilic

      A process is one that occurs at close to room temperature. Usually between 20°C to 40°C.

    8. even though the densely packed structure of highly crystallized PET greatly reduces the enzymatic hydrolysis of its ester linkages

      Vertommen et al. had shown that enzymes that help degrade PET act preferentially to the less organized, amorphous portions of the polymer, over the highly organized, crystalline portions.

    9. GenBank or Protein Data Bank

      GenBank is a database that is publicly available where scientists can record genetic sequences and the proteins they code for so that future researchers can use the information. Protein Data Bank focuses on recording and storing information on the shape of 3D molecules, particularly proteins.

    10. buffer

      A solution that prevents the pH from changing very much. A buffer is made of a weak acid and a weak base together in solution. If you add acid, it just reacts with the base. If you add base it reacts with the acid, preventing the pH from changing.

    11. μm

      Represents a micrometer, 10^-6 meters, or about the size of a single bacteria cell.

    12. polyesters

      A type of polymer that is used in many types of plastics. A polymer is a chemical made of one or more simple molecules, called monomers, bonded to itself many times in a repeating pattern. You may recognize polyester as the fabric that makes up some types of athletic wear.

    13. catabolic enzymes

      Catabolic reactions are those that break molecules into pieces, often giving off energy in the process. Enzymes are a type of protein that help speed up reactions. Therefore, catabolic enzymes help speed up reactions that turn large and complex molecules into smaller and more simple ones.

  2. Oct 2018
    1. turnover rate

      Describes how quickly an enzyme can take a single chemical through a specific chemical reaction. It is often abbreviated \(k_{cat}\) like you see here.

    2. cellular localization

      Describes where a molecule is in the cell. For example, a protein might be found in the cytoplasm, or it might hang out in a specific organelle.

    3. amino acid

      A small chemical that forms the monomer of a protein. Three base pairs in an open reading frame of DNA codes for one amino acid.

    4. esterases, lipases, or cutinases

      These are types of enzymes that are capable of breaking apart certain types of cell compounds. Esterases break down a wide range of compounds called esters. Lipases break down fats and cutinase hydrolyzes cutin, part of the waxy substance you find on leaves.

    5. We collected 250 PET debris–contaminated environmental samples including sediment, soil, wastewater, and activated sludge from a PET bottle recycling site (7). Using these samples, we screened for microorganisms that could use low-crystallinity (1.9%)

      The authors collected samples from different environments where PET plastic waste was likely to be found. In this case they chose to sample near a PET recycling plant. The plant specifically recycled high-crystallinity PET. They took some dirt, water, and sludge and put the samples in an environment including low-crystallinity PET. Low crystallinity PET is more disorganized and easier to break down than polymers with higher crystallinity.

      It was ultimately one of the samples of sediment that grew bacteria. When looking at the bacteria under a microscope, the researchers were able to see that it was growing on a thin layer of PET plastic.

    6. environmental remediation

      A process of repairing human-caused damage to the natural environment. For example, environmental remediation might involve removing harmful chemicals from water sources, or removing dangerous radioactive elements from soil. This work is looking at using biological organisms to remove PET film from the environment.

    7. Rare examples include members of the

      Previous work by Ronkvist et al. and Sulaiman et al. had shown that enzymes called cutinases could sometimes degrade PET if the temperature, polymer properties, and pH of the solution were right.

      Nimchua et al. found in two different studies that Fusarium oxysporum, a recently discovered fungus, and Fusarium solani, another fungus, produced the enzymes needed and were able to break down PET film.

      Link to Ronkvist et al: https://pubs.acs.org/doi/abs/10.1021/ma9005318

    8. Large quantities of PET have been introduced into the environment through its production and disposal,

      Plastic waste that ends up in the ocean can have a negative impact on aquatic wildlife. Furthermore, finding places to dispose of plastic on land can be challenging. Many countries are responding to the high levels of plastic pollution by regulating the use of single-use plastic.

      Read more about a recent agreement (2018) signed by many countries to combat ocean pollution: http://www.dw.com/en/g7-minus-two-leaders-agree-to-ocean-plastics-charter/a-44107774

    9. chemically inert

      Earlier, Smith et al. found minor degradation of PET by a few enzymes, along with no response by other, more common enzymes. Several labs determined that changing the structure of the polymer backbone to resemble more biodegradable polymers could make a new PET-like polymer biodegradable.

    10. reaction intermediate

      Sometimes a reaction occurs in more than one step. The original material reacts to form what we call a reaction intermediate, which may exist briefly or for a longer period of time, but is later turned into a final product.

      In this case, in simplified terms, PET is converted into reaction intermediate MHET (mono(2-hydroxyethyl) terephthalic acid), which is then converted to TPA (terephthalic acid) and EG (ethylene glycol).

    11. The catabolic genes for TPA and the metabolite protocatechuic acid (PCA) were up-regulated dramatically when cells were cultured on TPA-Na, BHET, or PET film. This contrasted with genes for the catabolism of maltose (Fig. 3A), which involves a pathway distinct from the degradation of TPA and EG, indicating efficient metabolism of TPA by I. sakaiensis. The transcript level of the PETase-encoding gene during growth on PET film was the highest among all analyzed coding sequences (table S4), and it was 15, 31, and 41 times as high as when bacteria were grown on maltose, TPA-Na, and BHET, respectively. This suggests that the expression of PETase is induced by PET film itself and/or some degradation products other than TPA, EG, MHET, and BHET.

      The authors measured which genes were being used when the l. sakaiensis cells were exposed to PET. They found that when PET film was present, the l. sakaiensis cells used the genes that make the PETase enzyme much more often then they used them when PET was not present.

      From this data, the authors concluded that either PET causes the cells to start making PETase or the enzyme production is induced by some degradation product of PET that they didn't test.

    12. Enzymatic degradation of polyesters is controlled mainly by their chain mobility

      Chain mobility is a measure of the flexibility of a polymer chain. A more flexible polymer chain will have higher chain mobility. In 2005, Marten et al. showed that polymers with lower chain mobilitites, including PET, are more challenging for enzymes to degrade.

    13. We compared the activity of the ISF6_4831 protein with that of three evolutionarily divergent PET-hydrolytic enzymes identified from a phylogenetic tree that we constructed using published enzymes (Fig. 2C and table S2). We purified TfH from a thermophilic actinomycete (10), cutinase homolog from leaf-branch compost metagenome (LC cutinase, or LCC) (11), and F. solanicutinase (FsC) from a fungus (fig. S5) (12), and we measured their activities

      The authors used published data of proteins having similar activity as the ISF6_4831 enzyme and analyzed it using statistical tests to select three enzymes that divergently evolved—meaning that the enzymes evolved from a common ancestor and accumulated enough differences to result in the formation of a new species.

    14. culture fluid

      The growing material, which contains water, inorganic minerals, and small organic molecules. Most of the microbes in the test tube attached to the PET film, making the liquid culture appear clear.

    15. ethylene glycol

      A chain of two carbon atoms between two oxygen atoms. When two ethylene glycol groups bond to either end of TPA, you get the MHET, the basic monomer of PET. You may have encountered ethylene glycol in the form of anti-freeze.

    16. 8. D. Ribitsch et al., Biocatalysis Biotransform. 30, 2–9 (2012).

      Rititsch et al. report cutinases from the bacteria Thermobifida alba. While the reported cutinases don't degrade PET particularly quickly, they do produce a novel degradation product.

      The authors were able to obtain a crystal structure, a type of picture on a molecular scale, of the enzyme degrading PET. This allowed them to identify parts of the enzyme that may be responsible for PET degradation.

    17. 1. V. Sinha, M. R. Patel, J. V. Patel, J. Polym. Environ. 18, 8–25 (2010).

      In this paper, Sinha et al. discuss the current best methods of disposing of and recycling plastic. The authors focus in particular on tertiary recycling techniques. These techniques use chemicals to break down the chemical bonds inside polymers.

  3. Sep 2018
    1. There are currently few known examples

      Earlier work found examples of enzymes that partially break down PET. These enzymes increased the hydrophilicity, or desire to dissolve in water, of PET. The previous work developed a range of different methods to measure PET modification from these enzymes, including SEM imaging, measuring the pH (which changes over the course of the degradation), and spectroscopy—a technique that involves shining different types of light at a sample and measuring what light passes through.

    2. durability, plasticity, and/or transparency have been industrially produced over the past century and widely incorporated into consumer products

      Sinha et al. (2010) detail the wide use of PET plastic, particularly in beverage bottles and describe possible methods of recycling. They focus particularly on tertiary, or chemical, recycling. Chemical recycling breaks down the polymer chain into smaller pieces using chemicals that are often harsh or corrosive. At the time Sinha et al.'s review was written, no biological methods of breaking down PET were known.

    3. cutin

      The polymer that makes up the waxy surfaces of leaves.

    4. heat-labile

      A compound that decomposes or stops functioning in response to increases in temperature. Proteins are often heat-labile, nonfunctional over a certain temperature.

    5. filamentous

      Refers to cells that form long tubes. Most types of fungi are filamentous.

    6. remediation

      A method of returning environments that have been damaged by human actions to a natural or healthy state.

  4. Aug 2018
    1. formed on the PET film upon culturing

      After collecting the samples the authors provided the samples with water, an appropriate temperature, and a food source of PET film. They later used microscopy to observe what samples were able to use the PET film as an energy source.

    2. This consortium degraded the PET film surface (fig. S1) at a rate of 0.13 mg cm–2 day–1 at 30°C (Fig. 1C), and 75% of the degraded PET film carbon was catabolized into CO2 at 28°C

      The data suggested that some organism that grows well in the soil around the PET recycling plant is responsible for degrading PET. The authors do not know at this point what organism is responsible or how the organism breaks down the PET fibers.

      Also note that the authors screened the different samples on low-crystallinity PET. PET is made with various degrees of crystallinity, or microscopic order, for different applications, and the authors cannot know from this data whether this same consortium would also be as effective at degrading higher-crystallinity film.

    3. hydrolyzing

      To hydrolyze a molecule is to break it into two pieces by adding a water molecule to it. Some chemicals undergo this process spontaneously, but in biological systems enzymes often help hydrolyze large biological molecules.

    4. enzymatically degrade

      Enzymes are large biological molecules that help speed up the transformation of one molecule into another. Degrading a polymer generally involves breaking it down into smaller pieces. Enzymatic degradation uses natural or lab-made enzymes to break down polymers that could harm the environment into something smaller and more benign.

    5. R. J. Müller, H. Schrader, J. Profe, K. Dresler, W. D. Deckwer, Macromol. Rapid Commun.

      The authors reported a hydrolase from Thermobifida fusca. The authors noted that the hydrolase successfully degrades PET. They note that it is helpful that PET has a glass transition temperature near the temperature where the enzyme can be incubated with the plastic.

    6. 3. D. Kint, S. Munoz-Guerra, Polym. Int. 48, 346–352 (1999).

      Discusses the synthetic methods of preparing biodegradable copolymers that include PET as well as the mechanisms that break down the resulting products.

      The review details several areas of research needed if PET copolymers are to become a feasible biodegradable material, including finding a polymer with sufficiently high melting point to be bonded to PET and ensuring the resulting copolymer has the correct properties for practical use.

    7. 5. T. Nimchua, H. Punnapayak, W. Zimmermann, Biotechnol. J. 2, 361–364 (2007).

      This paper took samples of fungi from a variety of tropical locations in Thailand and then tested them for cutinase production. It found 22 samples able to use a cutinase enzyme to degrade PET.

    8. T. Nimchua, D. E. Eveleigh, U. Sangwatanaroj, H. Punnapayak, J. Ind. Microbiol. Biotechnol. 35, 843–850 (2008)

      Reports on a fungus that is capable of turning PET yarn into terephthalic acid (TPA). The enzyme responsible was identified as a hydrolase. PET degradation was measured by the production of TPA and the increasing hydrophilicity of the PET fiber.

    9. lateral gene transfer

      When an organism picks up new DNA from another organism that is not its parent.

    10. Michaelis constant

      Indicates how much of a chemical per volume (concentration) in a solution with a given amount of enzyme needed to make the reaction go at half of its maximum possible rate.


    11. gene homologs

      Sets of DNA in different organisms that encode similar traits in different organisms. Homologs are often used to show how certain traits, like the ability to digest PET, developed over the course of evolution.

    12. Integr8 fully sequenced genome database

      A publicly accessible database with information gathered on all the DNA from all the organisms who have had their genome sequenced.

    13. gene cluster

      A section of DNA that contains information to build at least two proteins. Those proteins then perform related functions in a cell.

    14. transporter

      Types of proteins that go through a cell membrane. A transporter will help carry a molecule from the outside to the inside of a cell and vice versa.

    15. Extracellular

      A process that occurs outside of the cell.

    16. metabolism

      We often think of metabolism as the process by which humans break down food into energy; however, it can also be used to describe the process by which a cell breaks down a molecule, like PET in this case, for energy.

    17. transcriptomes

      The total population of mRNA in a cell. mRNA is the compound that helps carry information carried in DNA to the parts of the cell that use it to create proteins.

    18. RNA-sequenced

      Reads all of the RNA in a cell and records the order of base pairs.

    19. supernatant

      The liquid above a solid sample. In this case, the solid sample is composed of l. sakaiensis cells.

    20. glass transition temperature

      The temperature above which a polymer becomes flexible and pliable. Below the glass transition temperature the polymer will be hard and brittle, like glass.

    21. highly crystallized

      Indicating a material that is very ordered on a microscopic scale, like a grain of salt or a diamond. An amorphous solid, for example, lacks this order.

    22. BHET

      The basic monomer of PET. It is made up of TPA with two ethylene glycol groups attached to opposite ends.

    23. Bootstrap values

      Used to show what percent of times a node, or a place where two different branches originate, shows up in a phylogenic tree. The tree is recreated many times using slightly different data samples. Higher bootstrap values suggest the node is more likely to be correct.

    24. phylogenetic tree

      A diagram that shows how different organisms or biological species, like enzymes in this case, are related to each other. A node, where there is a branch in the tree, represents when the two species have evolutionarily diverged from each other.

    25. liquid chromatography

      A technique for separating different compounds. The compounds are dissolved in some solvent and run through a thin tube called a column lined with a solid substance. Compounds that are attracted to the solid substance come out of the column after the compounds that are less attracted to the solid in the sample.

    26. catalytic residues

      Amino acids that are directly involved with speeding up a reaction. In this case, the degradation of PET.

    27. open reading frame (ORF)

      A stretch of DNA that the cell is able to read and translate into mRNA which can be used to make a single protein.

    28. To explore the genes involved in PET hydrolysis in I. sakaiensis 201-F6, we assembled a draft sequence of its genome

      The authors took the DNA from Ideonella sakaiensis and created a list of the order of the DNA bases A, G, C, and T. Next, they used a computer program to compare the sequence to sequences from other organisms that were already known to degrade PET.

    29. secreted enzymes

      Enzymes that are built inside a cell, but later sent outside the cell. In this case, the secreted enzymes end up on the PET film.

    30. limiting dilutions

      A lab technique that isolates a single species of bacteria from a sample with more than one species of bacteria.

    31. SEM

      Stands for Scanning Electron Microscope. The microscope uses an electron beam that produces signals about the sample's surface and then converts that information into a picture. SEM allows us to see things too small to visualize with a more common light microscope.

    32. protozoa

      A type of single-celled organism. There is a lot of diversity among the different types of protozoa. Although they are single-celled like bacteria, they have different forms and behaviors. They typically lack a cell wall, for example, and many will survive by eating other organisms rather than by photosynthesis.

    33. morphological

      The morphology of a PET fiber describes its shape and surface texture. For example, we might describe its morphology as being rough, smooth, or flat. If there are morphological changes, that implies something about the bacteria changed the shape of the PET film.

    34. microbial consortium

      A set of microscopic organisms, typically bacteria, from two or more species.

    35. mineral medium

      A solution of water and whatever chemicals an organism, in this case these fungi, need to grow. It will often include vitamins, minerals, and some type of food source.

    36. Fusarium oxysporum and F. solani,

      These are types of fungi. Both fungi cause disease in some plants and F. solani also causes disease in humans. Previous research has shown that they can produce enzymes that can degrade PET to some extent.

    37. terephthalic acid

      The simplest form of the monomer, or repeating unit, of the polymer PET.

    38. aromatic

      Any compound that has six carbons bonded together in a ring and sharing three double bonds. Aromatic compounds tend to be unusually stable.

  5. Jul 2018
    1. 17. M. Hosaka et al., Appl. Environ. Microbiol. 79, 6148–6155 (2013).

      This paper reported two genes that code for two separate proteins that sit in a cell membrane and help TPA get into the cell.

  6. Jun 2018
    1. W. Zimmermann, S. Billig, Adv. Biochem. Eng. Biotechnol.

      This is a chapter in a book about biofunctionalization of polymers. The authors focus on how using biological methods to modify PET might make it more hydrophilic and therefore allow it to be used for a greater variety of applications in, for example, engineering and medicine.

      The authors do not focus on the use of methods of degrading polymers for recycling or disposal, however many of the biofunctionalization processes they describe involve degrading portions of PET polymer to give it better properties.

    2. ring-cleaved

      When a ring is cleaved, a set of atoms that were bonded together in a closed shape, like the hexagon in part B of the above figure, experience a bond breaking that opens up the closed shape.

    3. appendages

      We often think of appendages as being arms or leg in animals, but in bacteria they are thin tubes that emerge from the cell wall. Bacterial appendages help bacteria move and attach themselves to surfaces.