The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.

How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria

Ocean acidification due to anthropogenic CO2 emissions is a dominant driver of long-term changes in pH in the open ocean, raising concern for the future of calcifying organisms, many of which are present in coastal habitats. However, changes in pH in coastal ecosystems result from a multitude of drivers, including impacts from watershed pro- cesses, nutrient inputs, and changes in ecosystem structure and metabolism. Interaction between ocean acidification due to anthropogenic CO2 emissions and the dynamic regional to local drivers of coastal ecosystems have resulted in complex regulation of pH in coastal waters. Changes in the watershed can, for example, lead to changes in alkalinity and CO2 fluxes that, together with metabolic processes and oceanic dynamics, yield high-magnitude decadal changes of up to 0.5 units in coastal pH. Metabolism results in strong diel to seasonal fluctuations in pH, with characteristic ranges of 0.3 pH units, with metabolically intense habitats exceeding this range on a daily basis. The intense variability and multiple, complex controls on pH implies that the concept of ocean acidification due to anthropogenic CO2 emissions cannot be transposed to coastal ecosystems directly. Furthermore, in coastal ecosys- tems, the detection of trends towards acidification is not trivial and the attribution of these changes to anthropogenic CO2 emissions is even more problematic. Coastal ecosystems may show acidification or basification, depending on the balance betweenthe invasionof coastal waters byanthropogenic CO2, watershed export of alkalinity, organic matter and CO2 ,a nd changes in the balance between primary production, respira- tion and calcification rates in response to changes in nutrient inputs and losses of ecosystem components. Hence, we contend that ocean acidification from anthropogenic CO2 is largely an open-ocean syndrome and that a concept of anthro- pogenic impacts on marine pH, which is applicable across the entire ocean, from coastal to open-ocean environments, provides a superior framework to consider the multiple components of the anthropogenic perturbation of marine pH trajectories. The concept of anthropogenic impacts on seawater pH acknowledges that a regional focus is neces- sary to predict future trajectories in the pH of coastal waters and points at opportunities to manage these trajec- tories locally to conserve coastal organisms vulnerable to ocean acidification.

https://link.springer.com/content/pdf/10.1007%2Fs12237-013-9594-3.pdf

Is Ocean Acidification an Open-Ocean Syndrome? Understanding Anthropogenic Impacts on Seawater pH

Laccases are multicopper oxidases that catalyze the oxidation of a wide range of phenols or arylamines, and their use in industrial oxidative processes is increasing. We purified from the white rot fungus Trametes versicolor a laccase that exists as five different isozymes, depending on glycosylation. The 2.4 A resolution structure of the most abundant isozyme of the glycosylated enzyme was solved. The four copper atoms are present, and it is the first crystal structure of a laccase in its active form. The crystallized enzyme binds 2,5-xylidine, which was used as a laccase inducer in the fungus culture. This arylamine is a very weak reducing substrate of the enzyme. The cavity enclosing 2,5-xylidine is rather wide, allowing the accommodation of substrates of various sizes. Several amino acid residues make hydrophobic interactions with the aromatic ring of the ligand. In addition, two charged or polar residues interact with its amino group. The first one is an histidine that also coordinates the copper that functions as the primary electron acceptor. The second is an aspartate conserved among fungal laccases. The purified enzyme can oxidize various hydroxylated compounds of the phenylurea family of herbicides that we synthesized. These phenolic substrates have better affinities at pH 5 than at pH 3, which could be related to the 2,5-xylidine binding by the aspartate. This is the first high-resolution structure of a multicopper oxidase complexed to a reducing substrate. It provides a model for engineering laccases that are either more efficient or with a wider substrate specificity.

Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics.

The last step in the synthesis of lignin and suberin has been proposed to be catalyzed by peroxidases, although other proteins may also be involved. To determine which peroxidases are involved in the synthesis of lignin and suberin, five peroxidases from tomato (Lycopersicon esculentum) roots, representing the majority of the peroxidase activity in this organ, have been partially purified and characterized kinetically. The purified peroxidases with isoelectric point (pI) values of 3.6 and 9.6 showed the highest catalytic efficiency when the substrate used was syringaldazine, an analog of lignin monomer. Using a combination of transgenic expression and antibody recognition, we now show that the peroxidase pI 9.6 is probably encoded by TPX1, a tomato peroxidase gene we have previously isolated. In situ RNA hybridization revealed that TPX1 expression is restricted to cells undergoing synthesis of lignin and suberin. Salt stress has been reported to induce the synthesis of lignin and/or suberin. This stress applied to tomato caused changes in the expression pattern of TPX1 and induced the TPX1 protein. We propose that the TPX1 product is involved in the synthesis of lignin and suberin.

/pdf/a-tomato-peroxidase-involved-in-the-synthesis-of-lignin-and-3493eqronk.pdf

A Tomato Peroxidase Involved in the Synthesis of Lignin and Suberin

Biological approaches to tackle heavy metal pollution: A survey of literature

Rapid isoelectric focusing in a vertical polyacrylamide minigel system.

A dominant non-bacterial microorganism that may strongly impact environmental conditions in acid mine drainage at several Indiana coal mine sites is a single-celled protozoan, Euglena mutabilis. Field data suggest E. mutabilis has high tolerance for elevated total dissolved solids (TDS), to 18 g/l, and acid conditions to pH 1.7. Distribution is restricted to unmixed effluent pH<4.6, with prolific growth between pH 3.0 and 3.5. Additional factors influencing E. mutabilis include preference for areas with lower mineral/colloidal precipitation rates and a stable substrate of iron-rich precipitates. Initial studies indicate that in areas of prolific growth it contributes to oversaturation of dissolved oxygen by up to 200%. The presence of small orange intracellular crystalline-like structures, similar in color to iron oxyhydroxides, suggests that E. mutabilis may be sequestering iron, and possibly other metals. Further work is needed to determine if E. mutabilis contributes to natural mitigation of poor water quality at these and other coal mine sites.

Controls on the nature and distribution of an alga in coal mine-waste environments and its potential impact on water quality

Influence of water chemistry on the distribution of an acidophilic protozoan in an acid mine drainage system at the abandoned Green Valley coal mine, Indiana, USA

Biological activity of Euglena mutabilis , an acidophilic, photosynthetic protozoan, contributes to the formation of Fe-rich stromatolites in acid mine drainage systems. E. mutabilis is the dominant microbe in bright green benthic mats (biofilm), coating drainage channels at abandoned coal mine sites in Indiana. It builds biolaminates through phototactic and aerotactic behavior, similar to prokaryotes, by moving through precipitates that periodically cover the mats. E. mutabilis also contributes to formation of Fe-rich stromatolites by (1) intracellularly storing Fe compounds released after death, contributing to the solid material of stromatolites and acting as nucleation sites for precipitation of authigenic Fe minerals, and (2) generating O2 via photosynthesis that further facilitates precipitation of reduced Fe, any excess O2 not consumed by Fe precipitation being released to the atmosphere. Recognition of E. mutabilis –dominated biofilm in acidic systems raises a provocative hypothesis relating processes involved in formation of Fe-rich stromatolites by E. mutabilis to those responsible for development of Precambrian stromatolitic Fe formations and oxygenation of the early atmosphere.

Eukaryotic stromatolite builders in acid mine drainage: Implications for Precambrian iron formations and oxygenation of the atmosphere?

Adverse conditions in the acid mine drainage (AMD) system at the Green Valley mine, Indiana, limit diatom diversity to one species, Nitzschia tubicola. It is present in three distinct microbial consortia: Euglena mutabilis-dominated biofilm, diatomdominated biofilm, and diatom-exclusive biofilm. E. mutabilis dominates the most extensive biofilm, with lesser numbers of N. tubicola, other eukaryotes, and bacteria. Diatom-dominated biofilm occurs as isolated patches containing N. tubicola with minor fungal hyphae, filamentous algae, E. mutabilis, and bacteria. Diatom-exclusive biofilm is rare, composed entirely of N. tubicola. Diatom distribution is influenced by seasonal and intraseasonal changes in water temperature and chemistry. Diatoms are absent in winter due to cool water temperatures. In summer, isolated patchy communities are present due to warmer water temperatures. In 2001, the diatom community expanded its distribution following a major rainfall that temporarily diluted the effluent, creating hos...

H. K. Dannelly

Papers

Rapid isoelectric focusing in a vertical polyacrylamide minigel system.

Controls on the nature and distribution of an alga in coal mine-waste environments and its potential impact on water quality

Influence of water chemistry on the distribution of an acidophilic protozoan in an acid mine drainage system at the abandoned Green Valley coal mine, Indiana, USA

Eukaryotic stromatolite builders in acid mine drainage: Implications for Precambrian iron formations and oxygenation of the atmosphere?

Diatoms in Acid Mine Drainage and Their Role in the Formation of Iron-Rich Stromatolites