Tracking the molecular evolution of photosynthesis through characterization of atomic contents of the photosynthetic units

School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
Photosynthesis Research (Impact Factor: 3.5). 10/2008; 97(3):255-61. DOI: 10.1007/s11120-008-9356-4
Source: PubMed


Oxygen molecules have a great impact on protein evolution. We have performed a comparative study of key photosynthetic proteins in order to seek the answer to the question; did the evolutionary substitution of oxygen- and nitrogen-containing residues in the photosynthetic proteins correspond to nutrient constraints and metabolic optimization? The D1 peptide in RC II complexes has higher oxygen-containing amino acid residues and PufL/PufM have lower oxygen content in their peptides. In this article, we also discuss the possible influences of micro-environment and the available nutrients on the protein structure and their atomic distribution.

6 Reads
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: ENGLISH ABSTRACT: Grape and wine phenols consist of flavanols which is the building blocks for tannins. These building blocks are called monomers which consist of catechins, epicatechins, epigallocatechins and epicatechin-gallate. Tannin is important in wine as it contributes to bitterness, mouth feel (astringency) and maturation potential of the wine. Futhermore it has a health benefit as an antioxidant. Anthocyanins are responsible for the colour of red wine. The anthocyanins combine with tannins to form stable polymeric pigments. Due to the importance of tannins and anthocyanins in wine, it is imperitative that different winemaking techniques are used to extract as much of these components as possible and that the analysis is done quickly and accurately. The aim of this study was to evaluate different winemaking techniques and their extraction of tannins and anthocyanins into the wine. Too much tannin extraction can have a negative effect on the sensory quality of the wine. Therefore a second aim was to evaluate the mouth feel properties of a Shiraz wine. A third aim was to compare the two tannin precipitation methods in terms of time efficiency, repeatability and the ease of practice. To investigate the amount of tannin concentration extracted by different winemaking techniques, two cultivars (Cabernet Sauvignon and Shiraz) were used. These treatments included the addition of an enzyme during fermentation [E], cold maceration [CM], post maceration [PM] and the combination of cold and post maceration [CM+PM]. The grapes were harvested in two different climatic areas during the 2008 and 2009 vintages. The two climatic areas were classified according to the Winkler scale as a III (Morgenster) and a IV (Plaisir de Merle). The grapes were harvested at two different ripeness levels in order to evaluate the effect of the different winemaking processes on the extraction of tannins and anthocyanins. One harvest was before (LB) and the other after (HB) the commercial harvest. The results of this study showed significant differences in the phenolic composition of the wines. It was found that the warmer area showed higher tannin concentrations than the cooler area for both cultivars. In the 2008 Cabernet Sauvignon the CM extracted higher concentrations of tannin from the cooler area at both ripeness levels. In the warmer area, CM extracted the highest tannin concentration HB, but the CM+PM extracted the highest tannin concentration from Cabernet Sauvignon at the LB and CM at the HB of the warmer area. In 2009 the PM extracted the highest concentration of tannin at the lower ripeness level, while the E treatment extracted the highest concentration from the warmer area. In the cooler area the CM+PM extracted the highest concentration of tannin at a lower ripeness level, while there were no siginicant differences between the different treatments at the higher ripeness level. The highest anthocyanin concentration was found in the cooler area. The CM treatment was found to have no effect on anthocyanin extraction. Different methods are available to quantify the tannin concentration in wine. Two of the most popular tannin analytical methods are the bovine serum albumin (BSA) and the methyl cellulose precipitable tannin (MCP) methods. The BSA method is a very complex method which uses at least 3 times more reagents than the MCP method. The MCP method only analyzes tannins, while the BSA method analyzes tannins, monomeric pigments (MP), small polymeric pigments (SPP) and large polymeric pigments (LPP). In this study a good correlation was found between the two tannin precipitation methods (R2 – 0.88). There is controversy regarding the variability of these methods. Some scientists found that the two methods show a good correlation with HPLC, while others found that there was no such correlation between the precipitation methods and the HPLC. The MCP method had a practical advantage as it could be performed in half the time required for the BSA method. This has a significant impact in scenarios where a high sample throughput is required although it only measures total tannin. The phenolic composition and mouth feel of the wine was strongly influenced by the climatic area. In the warmer area the effect of tannin concentration on mouth feel was much less than in the cooler area. The wine made of riper grapes, was more grippy, bitter and numbing than the wines made from greener grapes. The E treatment was especially associated with a dry, grippy sensation. AFRIKAANSE OPSOMMING: Druif en wyn fenole bestaan uit flavanole wat weer die boublokke is van tanniene. Hierdie boublokke, wat bekend staan as monomere, betsaan uit katesjiene, epikatesjiene, epigallokatesjiene an epikatesjien-gallaat. Tanniene is belangrik in wyn aangesien dit bydra tot bitterheid, mondgevoel (vrankheid) asook die verouderingspotensiaal van wyn. As antioksidante hou dit ook gesondheidsvoordele in. Antosianiene dra by tot die kleur van rooiwyn. Antosianiene kombineer met tanniene om meer stabiele polimeriese pigmente te vorm. As gevolg van die belangrikheid van tanniene en antosianiene is dit van uiterse belang dat verskillende wynmaak tegnieke gebruik word om ekstraksie in die wyn te bevoordeel en dat die analitiese metode so vinnig en akkuraat as moontlik gedoen word. Die eerste doel van hierdie studie was om die ekstraksie van tanniene en antosianiene deur middel van verskillende wynmaak tegnieke te evalueer. Te veel tanniene in die wyn kan negatiewe sensoriese kwaliteit tot gevolg het. Daarom is die tweede doel om die sensoriese kwaliteit van Shiraz wyn te evalueer. Die derde doel van hierdie studie was die twee tannien presipitasie metodes met mekaar te vergelyk in terme van die moeilikheidsgraad van die metode, tyd doeltreffendheid en herhaalbaarheid. Verskillende wynmaak tegnieke (ensiem byvoegings [E], koue maserasie [CM], verlengde dopkontak [PM] en ‘n kombinasie van koue maserasie en verlengde dopkontak [CM+PM]) is vergelyk ten opsigte van tannien en antiosianien ekstraksie. In 2008 en 2009 is twee kultivars (Cabernet Sauvignon en Shiraz) in twee verskillende klimatologiese areas gepars. Hierdie areas is geklassifiseer in die Winklerskaal as ‘n IV (Plaisir de Merle) en ‘n III (Morgenster). Om die effek van die verskillende wynmaak tegnieke op die ekstraksie van antosianiene en tanniene te vergelyk, is hierdie twee kultivars by twee verskillende rypheidsgrade geoes. Die eerste oes was net voor kommersiële oes (LB) en die tweede oes het net na kommersiële oes (HB) plaasgevind. Die 2009 Shiraz wyn is organolepties beoordeel om die effek van die verskillende wynmaak tegnieke op die wyn se mondgevoel te vergelyk. Die resultate van hierdie studie toon beduidende verskille in die fenoliese samestelling van die wyne. Dit is gevind dat die warmer area hoër tannien konsentrasies het as die koeler area. In 2008 het die CM+PM die meeste tanniene uit die Cabernet Sauvignon geëkstraheer by LB en die CM by HB in die warmer area. Die CM het in die koeler area meer tanniene geëkstraheer by beide die LB en HB rypheidsgrade. In 2009 het PM die meeste tanniene geëkstraheer by LB terwyl E die meeste tanniene geëkstraheer in die warmer area. In die koeler area het CM+PM die meeste tanniene geëkstraheer, terwyl geen van die behandelings ‘n effek gehad het by HB. Die meeste antosianien konsentrasie was in die koeler area gevind as in die warmer area. In beide 2008 (LB en HB) en 2009 (LB) het CM die meeste antosianiene geëkstraheer, terwyl geen behandeling ‘n effek gehad het by HB. Twee van die mees populêre tannien analitiese metodes is die BSA (bovine serum albumien) en die MCP (metielsellulose presipitasie) metodes. Die BSA metode is ‘n baie meer ingewikkelde metode waarvoor drie keer meer reagense gebruik word as vir die MCP metode. Maar waar die MCP net tanniene ontleed, ontleed die BSA metode tanniene, monomere (MP), klein polimeriese pigmente (SPP) en groot polimeriese pigmente (LPP). Dit help indien daar gekyk wil word na die evolusie van polimeriese pigmente. In hierdie studie is bevind dat daar ‘n redelike korrelasie (R2 – 0.88) tussen die BSA en MCP metode bestaan. Die herhaalbaarheid van die metodes het redelike kontroversie veroorsaak, waar sommige navorsers bevind het dat die BSA metode nie so herhaalbaar is soos eers bevind is nie. Die MCP metode het ’n praktiese voordeel aangesien dit in die helfde van die tyd van die BSA metode uitgevoer kan word. Dit het ‘n groot impak indien ‘n groot hoeveelheid monsters ontleed moet word. Die fenoliese samestelling en mondgevoel word sterk beïnvloed deur die klimatologiese area. In die warmer area was die effek van tannien konsentrasie op mondgevoel kleiner as in die koeler area. Die wyn van ryper druiwe het meer harder, verdowingseffek en bitter nasmaak gehad as by die wyn van groener druiwe. Die ensiem behandeling was meer geassossieerd met droë mond gevoel. Thesis (MScAgric (Viticulture and Oenology))--University of Stellenbosch, 2011. Includes bibliography.
    Full-text · Article · Jan 2011
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional groups analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution.
    Full-text · Article · Nov 2013 · Gene