Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns-0

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns"</p><p>http://www.biomedcentral.com/1471-2164/8/412</p><p>BMC Genomics 2007;8():412-412.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216038.</p><p></p>nstructed by the NJ method using programs from the PHYLIP package (see Materials and Methods). Bootstrap values above 50 % (from 500 replicates) are shown above the individual branches, numbers below branches denote bootstrap values of a ML tree from the same input data. Gene names are color-coded according to the composition of the N-terminal domains of the encoded proteins (see Table 2). "Standard" proline-rich N-terminal domains (more than 20 % of Pro, Pro to Gly ratio larger than 2) are shown in black, glycine-rich N-terminal domains (more than 20 % of Gly, Gly to Pro ratio larger than 2) in green, N-terminal domains shorter than 10 amino acid residues in red. Among proteins with "standard" (Pro-rich) N-terminal domains, those with extremely long N-termini (over 80 residues) are shown in , those with increased contents of serine and threonine in , lysine-rich ones are , hydrophobic (A, V, L, I-rich) are marked by a plus (+) sign. An asterisk denotes a truncated N-terminus. Right: expression profiles of fourteen potato genes (see Table 1) in vegetative organs of cultured potato plants determined by semiquantitative PCR. Expression of the ef1a gene was used as the internal standard (products of PCR with 23 and 30 cycles are shown)

Top: multiple alignment of the conserved C-terminal domain sequences from representative HyPRPs of all major phylogenetic branches (see Figure 3)

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns"</p><p>http://www.biomedcentral.com/1471-2164/8/412</p><p>BMC Genomics 2007;8():412-412.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216038.</p><p></p> At – , Le – , Mt – , Os – , Pt – , St – , Zm – . Residues conserved between at least 75 % of the depicted sequences are shown on black background, positions with conserved amino acid properties on gray background. Conserved cysteines are shown in red and denoted by numbers, selected substitutions at the conserved cysteine positions are highlighted in blue. Bottom: consensus sequence expressed as a PROSITE – style pattern that detects most HyPRPs and no false positives

Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns-4

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns"</p><p>http://www.biomedcentral.com/1471-2164/8/412</p><p>BMC Genomics 2007;8():412-412.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216038.</p><p></p>BioEdit) suggests a possible mechanism of independent acquisition of Gly-rich N-termini by inversion of a region encoding a part of a conventional Pro-rich domain. Triplets encoding glycine (when read left to right) are shown in red letters, while those encoding proline on the opposite strand are highlighted in gray (dark and bright shades used to distinguish individual triplets). Nucleotides conserved in at least two thirds of the sequences are shown in bold and marked by dots, absolutely conserved positions are marked by asterisks. Note the generally low degree of sequence conservation

Left: an unrooted consensus phylogenetic tree (cladogram) of nucleotide sequences encoding the conserved C-terminal domains of HyPRPs from potato and , constructed by the ML method (see Materials and Methods)

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns"</p><p>http://www.biomedcentral.com/1471-2164/8/412</p><p>BMC Genomics 2007;8():412-412.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216038.</p><p></p> Bootstrap values above 50 % (from 500 replicates) are shown above the individual branches, numbers below branches denote bootstrap values of a NJ tree from the same input data. The ML and NJ trees agreed in all clades with bootstrap support over 50 % with exception of (i) swapping St1 and At1g62500 and (ii) swapping At4g15160 and At4g15160, in both cases with NJ bootstrap values below 76 %. loci are denoted by standard AGI locus identifiers. Gene names are color-coded and typographically marked according to the composition of the N-terminal domains of the encoded proteins as in Figure 1; in addition, proline- and glycine-rich N-terminal domains (not fitting into the categories of proline- or glycine-rich, but containing more than 10 % of each of these amino acids) are shown in blue. genes with reliable potato orthologues are denoted by black filled squares, chromosomal clusters and tandem duplications are marked by chromosome cluster numbers to the right of the tree (see Additional file ). Right: expression profiles of selected genes according to the publicly available expression data: top – orthologues of potato genes (with potato expression patterns from Figure 1 for comparison; apical stems shown in the "shoot apex" position), bottom – genes from the four chromosomal clusters. Order of genes within each cluster corresponds to that in the tree

The disadvantages of being a hybrid during drought: A combined analysis of plant morphology, physiology and leaf proteome in maize

<div><p>A comparative analysis of various parameters that characterize plant morphology, growth, water status, photosynthesis, cell damage, and antioxidative and osmoprotective systems together with an iTRAQ analysis of the leaf proteome was performed in two inbred lines of maize (<i>Zea mays</i> L.) differing in drought susceptibility and their reciprocal F1 hybrids. The aim of this study was to dissect the parent-hybrid relationships to better understand the mechanisms of the heterotic effect and its potential association with the stress response. The results clearly showed that the four examined genotypes have completely different strategies for coping with limited water availability and that the inherent properties of the F1 hybrids, <i>i</i>.<i>e</i>. positive heterosis in morphological parameters (or, more generally, a larger plant body) becomes a distinct disadvantage when the water supply is limited. However, although a greater loss of photosynthetic efficiency was an inherent disadvantage, the precise causes and consequences of the original predisposition towards faster growth and biomass accumulation differed even between reciprocal hybrids. Both maternal and paternal parents could be imitated by their progeny in some aspects of the drought response (<i>e</i>.<i>g</i>., the absence of general protein down-regulation, changes in the levels of some carbon fixation or other photosynthetic proteins). Nevertheless, other features (<i>e</i>.<i>g</i>., dehydrin or light-harvesting protein contents, reduced chloroplast proteosynthesis) were quite unique to a particular hybrid. Our study also confirmed that the strategy for leaving stomata open even when the water supply is limited (coupled to a smaller body size and some other physiological properties), observed in one of our inbred lines, is associated with drought-resistance not only during mild drought (as we showed previously) but also during more severe drought conditions.</p></div

The gas exchange and water use characteristics of the leaves of drought-stressed maize genotypes.

<p>The net photosynthetic rate (P_N) (<b><i>A</i></b>), intercellular CO₂ concentration (c_i) (<b><i>B</i></b>), net transpiration rate (E) (<b><i>C</i></b>), stomatal conductance (g_S) (<b><i>D</i></b>), water use efficiency (WUE) (<b><i>E</i></b>) and relative water content (RWC) (<b><i>F</i></b>) in the leaves of two maize genotypes (2023 and CE704) that were subjected to 6 days of drought (solid bars) or normally watered (hatched bars). The means ± SD (n  = 18) are shown. The letters <i>a-c</i> denote the statistical significance (as determined by the Tukey-Kramer test) of the differences between genotypes/water treatments (only those marked with different letters differ significantly at p≤0.05).</p

The morphology and biomass characteristics of drought-stressed maize genotypes.

<p>The number of fully developed leaves (<b><i>A</i></b>), the plant height (<b><i>B</i></b>), the total area of the photosynthetically active leaves (<b><i>C</i></b>), the leaf area ratio (LAR) (<b><i>D</i></b>), the shoot fresh mass (FM) (<b><i>E</i></b>), the shoot dry mass (DM) (<b><i>F</i></b>), the root fresh mass (<b><i>G</i></b>) and the root dry mass (<b><i>H</i></b>) of maize inbred lines 2023 (23) and CE704 (04) and their F1 hybrids 2023×CE704 (23×04) and CE704×2023 (04×23) subjected to 10 days of drought (solid bars) or normally watered (hatched bars). Means ± SD (n = 20) are shown. The letters <i>A-C</i> denote the statistical significance of the differences between genotypes under control conditions, the letters <i>a-c</i> denote the statistical significance of the differences between genotypes under drought conditions (only those marked with different letters differ significantly at p ≤ 0.05). Asterisks indicate significant differences between control and drought-stressed plants of the respective genotype (p ≤ 0.05).</p

Five proteins that showed the highest negative uniparental heterosis in maize F1 hybrids 2023×CE704 or CE704×2023 after 10 days of drought.

<p>Five proteins that showed the highest negative uniparental heterosis in maize F1 hybrids 2023×CE704 or CE704×2023 after 10 days of drought.</p

The 2D gels showing the leaf proteomes of drought-stressed and control plants of two maize genotypes.

<p>S: drought-stressed; C: control; 2023: sensitive genotype; CE704: tolerant genotype. Only selected regions of the gels are shown; the frames mark the differences in the representation of two isoforms of the heat-shock protein HSP26 (spots nos. 4 and 5) in the drought-stressed plants of both genotypes. The protein spots that are differentially represented between genotypes and water treatments are marked by arrows and the respective numbers (1–11; N … unidentified protein) refer to the notation used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038017#pone-0038017-t003" target="_blank">Table 3</a>.</p

The differences in leaf proteins observed either between the genotypes or between control (C) and drought-stressed (S) plants of 2023 and CE704 maize genotypes, as evaluated by the 2D-electrophoresis method.

<p>AT  =  <i>Arabidopsis thaliana</i> (L.) Heynh.; ETC  =  electron transport chain; OEC  =  oxygen evolving complex of photosystem II; OS  =  <i>Oryza sativa</i> L.; LE  =  <i>Lycopersicon esculentum</i> Mill.; TA  =  <i>Triticum aestivum</i> L.; ZM  =  <i>Zea mays</i> L. The following symbols indicate the quantity of individual spots: –  =  absence, +/−  =  very weak intensity, +  =  medium intensity, ++  =  high intensity.</p