The dead, hardened floral bracts of dispersal units of wild wheat function as storage for active hydrolases and in enhancing seedling vigor

It is commonly assumed that the dead, hardened floral bracts of the dispersal unit of grasses have been evolved to protect seeds from predation and / or assist in fruit/caryopsis dispersal. While these structures have important agronomical and economical implications, their adaptive value has not been fully explored. We investigated the hypothesis that the maternally derived hardened floral bracts have been evolved not just as a means for caryopsis protection and dispersal, but also as storage for substances that might affect seed germination and seedling vigor. Dead glumes as well as lemmas and paleas of wild emmer wheat (Triticum turgidum var dicoccoides) were found to store and release upon hydration active hydrolases including nucleases and chitinases. High nuclease activity was released upon hydration from glumes derived from wild strains of wheat including Triticum urartu and wild emmer wheat, while very low nuclease activity was detected in glumes derived from domesticated, free-threshing wheat cultivars (e.g., durum wheat). Germination from the intact dispersal unit of wild emmer wheat was delayed, but post germination growth was better than those of separated caryopses. Most notable was a significant increase in lateral root production on seedlings germinated from the intact dispersal unit. Proteome analysis of wild emmer wheat glumes revealed many proteins stored and released upon hydration including S1-type nucleases, peptidases, antifungal hydrolases such as chitinases and β-1,3-glucanase as well as pectin acetylesterase, a protein involved in cell wall degradation and remodeling. Also, reactive oxygen species (ROS)-detoxifying enzymes such as superoxide dismutase and ascorbate peroxidase were overrepresented in dead glumes of wild emmer wheat. Thus our study highlighted previously unknown features of the dispersal unit in wild wheat in which the dead, hardened floral bracts enclosing the caryopsis store active hydrolases and nutritional elements and probably growth promoting substances that facilitate seed longevity and germination and increase seedling vigor.

• For Sequest results, the score is the sum of all peptide Xcorr values above the specified score threshold. The score threshold is calculated as follows:

+ peptide_charge × peptide_relevance_factor
where peptide_relevance_factor is an advanced parameter of the SEQUEST or Sequest HT node in the "Protein Scoring Option" category with a default value of 0.4. For each spectrum, only the highest-scoring match is used.
For each spectrum and sequence, the Proteome Discoverer application uses only the highest scored peptide. When it performs a search using dynamic modifications, one spectrum might have multiple matches because of permutations of the modification site.

Score, continued
• For Mascot results, the score is: -Standard score, which is the cumulative protein score based on summing the ion scores of the unique peptides identified for that protein. If a peptide was redundantly identified, only the highest-scoring peptide is used.
-or--MudPIT score, which is the sum of the "excess of ions" score over the homology or identity threshold for each spectrum plus the average threshold. For MudPIT scoring, the score for each peptide is not its absolute score but the amount that it is above the threshold. Therefore, peptides with a score below the threshold do not contribute to the score. For each peptide, the threshold is the homology threshold, if it exists; otherwise, it is the identity threshold. Separating proteins by molecular weight can be one of the steps in twodimensional gel electrophoresis. You can use the protein's molecular weight as a rough constraint to estimate whether it is reasonable to identify a particular protein in a certain fraction that was searched.
calc. pI Displays the theoretically calculated isoelectric point, which is the pH at which a particular molecule carries no net electrical charge.
The amino acids that make up proteins can be positive, negative, neutral, or polar in nature, and together they give a protein its overall charge. At a pH below their isoelectric point, proteins carry a net positive charge; at a pH above their isoelectric point, they carry a net negative charge. Gel electrophoresis can then separate proteins according to their isoelectric point (overall charge) with a polyacrylamide gel, using a technique called isoelectric focusing, which uses a pH gradient to separate proteins. Isoelectric focusing is also the first step in two-dimensional gel polyacrylamide gel electrophoresis.
When you have searched the fractions resulting from isoelectric focusing, you can use the calc. pI value to estimate whether you might expect to find a particular protein in the given fraction. Clicking the plus (+) sign next to any protein opens the column parameters for the associated peptides. For descriptions of these parameters, see Peptides Page Parameters.

Feature Description
Sequence Displays the sequence of amino acids that compose the peptide.

# PSMs
Displays the total number of identified peptide sequences (PSMs) for the protein, including those redundantly identified.

Protein Group Accessions
Displays the unique identifiers (accessions) of all master proteins from all protein groups that include this peptide sequence.
The identifiers displayed in the Protein Group Accessions column are the same as those displayed in the Accession column on the Proteins page. They are also the same identifiers displayed when you click + to the left of a peptide on the Peptides page to display proteins.

# Proteins
Displays the number of proteins in which this peptide is found.
# Protein Groups Displays the number of protein groups in which this peptide is found.

Modifications
Displays the static and dynamic modifications identified in the peptide.

XCorr (searchdependent)
Scores the number of fragment ions that are common to two different peptides with the same precursor mass and calculates the cross-correlation score for all candidate peptides queried from the database (Sequest searches only).

Expectation Value or Exp Value (Mascot only)
Displays the expectation value, which is a measure of the number of matches with scores equal to or better than the score values that are expected to occur only by chance. For Mascot, the smaller the expectation value is, the better the match is considered.

IonScore (Mascot only)
Refer to the Mascot documentation from Matrix Science.
Δ Score Displays a measure of the difference between the top two scores for the peptides identified by that spectrum. The Proteome Discoverer application calculates this score as follows. For a detailed discussion of the delta score calculation, see Calculating the Delta Score.

Rank
Displays the ordering of peptides by rank. Indicates why a peptide was used in quantification or why it was not: •No Quan Values: No isotopic or isobaric labels were detected in the sample.
•No Quan Labels: The peptide was not modified by a label.
• Redundant: The same MS/MS spectra were used for two separate peptide matches.
• No Proteins: The peptide is not associated with a protein, probably because it did not go above the cutoff threshold defined by the search engines, using these parameters: the Protein Relevance Threshold or Protein Relevance Factor parameter in Mascot or the Protein Relevance Threshold parameter in Sequest.
• Unique: The same MS/MS spectra were used for one peptide match, and the peptide belongs to one protein.
•Not Unique: The peptide was found in another protein.
• Indistinguishable Channels: The peptide does not have amino acids that could have the specified labels or it has the specified labels but has defined channels with the same delta masses, rendering the channels indistinguishable.
• Excluded by Method: Peptides or quantification results are excluded from protein quantification according to the Single-Peak/Missing Channels Allowed setting in the quantification method. This setting specifies the allowed number of missing quantification channels or single-peak quantification channels that can be included in valid quantification results in the ratio calculation. Indicates whether the peptide was used to quantify the protein: •Used: The peptide was used in quantification.
•Not Used: The peptide was not used in quantification.
Heavy/Light (in MSF files with precursor ion quantification results only) Displays the isotopic label type. This column appears only when you have loaded an MSF file containing the results of isotopically labeled quantification.
Ratio columns (in MSF files with reporter ion quantification results only) Display the corrected ratio of the intensity of the fragmented tag in a sample to the intensity of the fragmented tag in the control sample.

Intensity
Displays the intensity of the precursor ion.

m/z [Da]
Displays the mass-to-charge ratio of the precursor ion, in daltons.

MH+ [Da]
Displays the protonated monoisotopic mass of the peptides, in daltons.

Δ M [ppm]
Displays the difference between the theoretical mass of the peptide and the experimental mass of the precursor ion.

RT [min]
Displays the retention time when the peptide was observed, in minutes.

Binomial Peptide Score
Displays a peptide score based on the cumulative binomial probability that the observed match is a random event. The value of the Binomial Peptide score heavily depends on the data scored, but usually scores above 50 indicate a good PSM.

Isoform Confidence Probability
Estimates the probability (0-100%) that the isoform is correct.

phosphoRS Site Probabilities
Estimates the probability (0-100%) of each phosphorylation site being truly phosphorylated. phosphoRS probabilities above 75% indicate that a site is truly phosphorylated.