Evolutionary traces decode molecular mechanism behind fast pace of myosin XI

<p>Abstract</p> <p>Background</p> <p>Cytoplasmic class XI myosins are the fastest processive motors known. This class functions in high-velocity cytoplasmic streaming in various plant cells from algae to angiosperms. The velocities at which they process are ten times faster than its closest class V homologues.</p> <p>Results</p> <p>To provide sequence determinants and structural rationale for the molecular mechanism of this fast pace myosin, we have compared the sequences from myosin class V and XI through Evolutionary Trace (ET) analysis. The current study identifies class-specific residues of myosin XI spread over the actin binding site, ATP binding site and light chain binding neck region. Sequences for ET analysis were accumulated from six plant genomes, using literature based text search and sequence searches, followed by triple validation <it>viz</it>. CDD search, string-based searches and phylogenetic clustering. We have identified nine myosin XI genes in sorghum and seven in grape by sequence searches. Both the plants possess one gene product each belonging to myosin type VIII as well. During this process, we have re-defined the gene boundaries for three sorghum myosin XI genes using fgenesh program.</p> <p>Conclusion</p> <p>Molecular modelling and subsequent analysis of putative interactions involving these class-specific residues suggest a structural basis for the molecular mechanism behind high velocity of plant myosin XI. We propose a model of a more flexible switch I region that contributes to faster ADP release leading to high velocity movement of the algal myosin XI.</p

Structural insights on Sucrose transport by Oryza sativa L. Sucrose/H+ Symporter1 (OsSUT1) through refined sequence - template alignment based structural modelling

Sucrose/H+ Symporters (SUTs) play an important role in plant growth and yield. They are involved in long distance transport of sucrose from source leaves to filling grains of cereals through a process called phloem loading. However, the molecular mechanism of sucrose transport through SUTs is not yet known. Understanding the key residues involved in sucrose transport can be helpful in developing high yielding varieties through genetic engineering, gene editing or allele mining. Here, the molecular model of OsSUT1 developed based on refined target-template alignment using Modeller software provides structural insights on the sucrose transport mechanism. We propose 13 putative sucrose binding residues and 11 putative H+ binding residues involved in sucrose/H+ co-transport in OsSUT1

Structural insights on Sucrose transport by Oryza sativa L. Sucrose/H+ Symporter1 (OsSUT1) through refined sequence - template alignment based structural modelling

283-290Sucrose/H+ Symporters (SUTs) play an important role in plant growth and yield. They are involved in long distance transport of sucrose from source leaves to filling grains of cereals through a process called phloem loading. However, the molecular mechanism of sucrose transport through SUTs is not yet known. Understanding the key residues involved in sucrose transport can be helpful in developing high yielding varieties through genetic engineering, gene editing or allele mining. Here, the molecular model of OsSUT1 developed based on refined target-template alignment using Modeller software provides structural insights on the sucrose transport mechanism. We propose 13 putative sucrose binding residues and 11 putative H+ binding residues involved in sucrose/H+ co-transport in OsSUT1

Evolution of protein domain architectures

This chapter reviews current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this will directly impact which domain architectures can be formed in different species. Studies relating domain family size to occurrence have shown that they generally follow power law distributions, both within genomes and larger evolutionary groups. These findings were subsequently extended to multi-domain architectures. Genome evolution models that have been suggested to explain the shape of these distributions are reviewed, as well as evidence for selective pressure to expand certain domain families more than others. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain arrangements. Following this, we review inferences of ancestral domain architecture and the conclusions concerning domain architecture evolution mechanisms that can be drawn from these. Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly). We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution

PHYSICOCHEMICAL STABILITY OF SELECTED FROZEN AND DEHYDRATED FOODS: IN RELATION TO STATE/PHASE TRANSITIONS

Water activity (aw) concept is traditionally used as a predictive means for microbial, chemical and physical changes in low and intermediate moisture. State of water and food solids, state and phase transitions are also relevant in explaining physicochemical stability of in non-equilibrium food systems as observed by many researchers. However, the relationship between the state and phase transitions and rate of physicochemical degradation reactions in food systems is still not apparent. The broad objective of this research is to evaluate the physicochemical stability of selected dehydrated and frozen food systems in relation to state and phase transitions.Water sorption isotherms were developed by isopiestic method and glass transition temperatures of raspberries were determined by differential scanning calorimetry to identify with the interactions between water and food solids. A state diagram of raspberry was developed, which included glass line; glass transition temperature versus solids content, freezing curve; initial freezing point versus solids content; end point of freezing Tm', corresponding solids content Xs', characteristic glass transition Tg' and corresponding solids contents Xs" of maximally-freeze-concentrated raspberry. Water activity varied significantly at equivalent water concentrations obtained using absorption or desorption however, the glass transition temperatures of raspberries were independent on the method of equilibration.Enthalpy relaxation experiments were conducted in freeze-dried raspberry powder at selected temperatures below its onset glass transition temperature (Tgi) to explore the molecular relaxation process as many physicochemical degradations continue to occur in the glassy state. A larger mean enthalpy relaxation time for raspberry powder at temperatures lower than the Tg suggests molecular level relaxations are much slower at temperatures smaller than Tg. Anhydrous glucose maltose and maltotriose were used to investigate the effect of molecular weight on enthalpy relaxation. Maltotriose may be a better encapsulant or food ingredient than glucose and maltose to reduce structural relaxation and protect bioactive compounds in raspberries during their glassy state storage of food systems as smaller relaxation enthalpies are observed at isothermal aging.Anthocyanin degradation in frozen and freeze-dried raspberries during storage was examined in relation to state/phase transition temperatures. Anthocyanin degradation was significantly greater in rubbery state of freeze-dried raspberries in comparison to the glassy state while state of the system did not influence anthocyanin degradation in frozen raspberries. The influence of state/phase transitions and temperature fluctuations on ice recrystallization during the frozen storage of salmon fillets was systematically investigated by observing the change in ice crystal size. Ice recrystallization was observed in the glassy state of frozen salmon, however, the rate was significantly smaller than that in the rubbery state due to the reduced mobility of unfrozen water. The influence of state/phase transition on physicochemical stability is largely dependent on the nature of food system and type of physicochemical degradation. The findings of this research are important to food industries because they can help optimize storage and distribution conditions and minimize quality loss in dehydrated and frozen foods

Glass transition influence on ice recrystallization in Atlantic salmon (Salmo Salar) during frozen storage

Low temperature transitions may occur in frozen foods due to the temperature fluctuations resulting in less viscous and partially melted food matrices; In the current study, the influence of glass transitions and temperature fluctuations on ice recrystallization during the frozen storage of salmon fillet was systematically investigated; The characteristic glass transition temperature (Tg') and onset temperature of ice crystal melting (Tm') in salmon determined using a modulated differential scanning calorimeter (MDSC) were -27 and -17oC, respectively; The temperature (T = -35oC) of frozen salmon fillets was modulated within glassy state (TTm'), by exposing the trays to room temperature (23oC) for predetermined periods (2 to 26 min) twice a day during the four weeks of storage; The characterization of ice crystals was conducted by observing the cavities formed after sublimation of ice crystals using (a) Environmental scanning electron microscopy (ESEM) (b). X-ray computed tomography (XCT); Ice crystal growth was observed in frozen salmon in the glassy state; however the ice crystal size was greatest in the rubbery state (when the temperature fluctuation resulted in temperature above Tm'); The findings of this study are important to the frozen food industries in optimizing the storage and distribution conditions to minimize textural quality loss due to recrystallization

Water Diffusion from a Bacterial Cell in Low‐Moisture Foods

We used a Fick's unsteady state diffusion equation to estimate the time required for a single spherical shaped bacterium (assuming Enterococcus faecium as the target microorganism) in low-moisture foods to equilibrate with the environment. We generated water sorption isotherms of freeze-dried E. faecium. The water activity of bacterial cells at given water content increased considerably as temperature increased from 20 to 80 °C, as observed in the sorption isotherms of bacterial cells. When the water vapor diffusion coefficient was assumed as between 10(-12) and 10(-10) m(2) /s for bacterial cells, the predicted equilibration times (teq ) ranged from 8.24×10(-4) to 8.24×10(-2) s. Considering a cell membrane barrier with a lower water diffusion coefficient (10(-15) m(2) /s) around the bacterial cell with a water diffusion coefficient of 10(-12) m(2) /s, the teq predicted using COMSOL Multiphysics program was 3.8×10(-1) s. This result suggests that a single bacterium equilibrates rapidly (within seconds) with change in environmental humidity and temperature

Water Diffusion from a Bacterial Cell in Low-Moisture Foods

We used a Fick's unsteady state diffusion equation to estimate the time required for a single spherical shaped bacterium (assuming Enterococcus faecium as the target microorganism) in low-moisture foods to equilibrate with the environment. We generated water sorption isotherms of freeze-dried E. faecium. The water activity of bacterial cells at given water content increased considerably as temperature increased from 20 to 80 °C, as observed in the sorption isotherms of bacterial cells. When the water vapor diffusion coefficient was assumed as between 10(-12) and 10(-10) m(2) /s for bacterial cells, the predicted equilibration times (teq ) ranged from 8.24×10(-4) to 8.24×10(-2) s. Considering a cell membrane barrier with a lower water diffusion coefficient (10(-15) m(2) /s) around the bacterial cell with a water diffusion coefficient of 10(-12) m(2) /s, the teq predicted using COMSOL Multiphysics program was 3.8×10(-1) s. This result suggests that a single bacterium equilibrates rapidly (within seconds) with change in environmental humidity and temperature

Structural and Functional Insights on the Myosin Superfamily

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