Regulation of Protein Degradation

The TGN/EE SNARE protein SYP61 and the ubiquitin ligase ATL31 cooperatively regulate plant responses to carbon/nitrogen conditions in Arabidopsis

Ubiquitination is a post-translational modification involving the reversible attachment of the small protein ubiquitin to a target protein. Ubiquitination is involved in numerous cellular processes, including the membrane trafficking of cargo proteins. However, the ubiquitination of the trafficking machinery components and their involvement in environmental responses are not well understood. Here, we report that the Arabidopsis thaliana trans-Golgi network/early endosome localized SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein SYP61 interacts with the transmembrane ubiquitin ligase ATL31, a key regulator of resistance to disrupted carbon (C)/nitrogen/(N)-nutrient conditions. SYP61 is a key component of membrane trafficking in Arabidopsis. The subcellular localization of ATL31 was disrupted in knockdown mutants of SYP61, and the insensitivity of ATL31-overexpressing plants to high C/low N-stress was repressed in these mutants, suggesting that SYP61 and ATL31 cooperatively function in plant responses to nutrient stress. SYP61 is ubiquitinated in plants, and its ubiquitination level is upregulated under low C/high N-nutrient conditions. These findings provide important insights into the ubiquitin signaling and membrane trafficking machinery in plants.

Effects of active and passive modified atmosphere packaging on biochemical properties of cut Dendrobium orchid flowers

Optimal storage conditions are essential to preserving the quality of postharvest produce and cut flowers during transportation, especially to overseas destinations. As a result, this research investigated the effects of active and passive modified atmosphere packaging (MAP) on the biochemical properties of cut Dendrobium Sonia orchid flowers. In active MAP, the orchid flowers were wrapped in MAP plastic film filled with 5 % carbon dioxide (CO₂) and 2 % oxygen (O₂). Meanwhile, in passive MAP the flowers were stored inside MAP plastic film without filling with 5 % CO₂ and 2 % O₂. The experimental MAP plastic films were polyethylene, low density polyethylene, high density polyethylene, polypropylene, and polyvinyl chloride films. The biochemical parameters included storage life, respiration rate, ethylene production, internal O₂ and CO₂, anthocyanin content, protein degradation, and electrolyte leakage. The results showed that the average storage life of orchid flowers under passive MAP condition was 9–15 days, depending on the plastic film types. The longest storage life of 15.66 days was achieved with polypropylene film. The storage life of orchid flowers in active MAP was 9.33 days on average. Without MAP (control), the storage life was 7 days under normal atmosphere condition (0.03 % CO₂ and 21 % O₂). The experiments also demonstrated that MAP efficiently reduced respiration rate, ethylene production, anthocyanin degradation, protein degradation, and electrolyte leakage. Unlike existing research on MAP which focused primarily on extending the shelf life of fresh produce or cut flowers, this study comparatively investigated the biochemical properties of cut orchid flowers stored in MAP environment, in addition to the storage life.

Effects of high CO2 and low O2 on biochemical changes in cut Dendrobium orchids

Exportation of cut flowers entails long distance transportation, and the quality of cut flowers deteriorates as the distance and transportation time increase. Low storage temperatures and modified atmosphere are commonly used to extend the life of cut flowers. As a result, this research explored the potential use of high CO₂ and low O₂ to prolong the shelf life of cut flowers. Specifically, this study examined the effects of high CO₂ and low O₂ storage on the biochemical changes in cut Dendrobium pink stripe orchid flowers. The experiments were conducted under normal and high CO₂ and low O₂ conditions, and results were compared. Under the normal condition, carbon dioxide (CO₂) and oxygen (O₂) concentrations were 0.03 % and 21 %. In the high CO₂ and low O₂ environment, CO₂ was varied between 5 and 10 %; and O₂ between 2, 4, 6, and 8 %. The storage temperature and relative humidity were 13 °C and 95 %. The originality of this work is the use of high CO₂ and low O₂ storage environments to investigate the biochemical changes in cut Dendrobium orchid flowers. The experimental results showed that high CO₂ and low O₂ significantly enhanced the storage life of Dendrobium orchid flowers (p < 0.05). The longest storage life of 28.33 days was achieved under 5 % CO₂ and 2 % O₂ atmosphere condition, compared with 11.67 days under the normal atmosphere condition. High CO₂ and low O₂ storage also helped to retain total anthocyanin content while lowering fresh weight loss, respiration rate, ethylene production, protein degradation, and protease activity.

Transcription Factor bHLH2 Represses CYSTEINE PROTEASE77 to Negatively Regulate Nodule Senescence

Legume-rhizobia symbiosis is a time-limited process due to the onset of senescence, which results in the degradation of host plant cells and symbiosomes. A number of transcription factors, proteases, and functional genes have been associated with nodule senescence; however, whether other proteases or transcription factors are involved in nodule senescence remains poorly understood. In this study, we identified an early nodule senescence mutant in Medicago truncatula, denoted basic helix-loop-helix transcription factor2 (bhlh2), that exhibits decreased nitrogenase activity, acceleration of plant programmed cell death (PCD), and accumulation of reactive oxygen species (ROS). The results suggest that MtbHLH2 plays a negative role in nodule senescence. Nodules of wild-type and bhlh2-TALEN mutant plants at 28 d postinoculation were used for transcriptome sequencing. The transcriptome data analysis identified a papain-like Cys protease gene, denoted MtCP77, that could serve as a potential target of MtbHLH2. Electrophoretic mobility shift assays and chromatin immunoprecipitation analysis demonstrated that MtbHLH2 directly binds to the promoter of MtCP77 to inhibit its expression. MtCP77 positively regulates nodule senescence by accelerating plant PCD and ROS accumulation. In addition, the expression of MtbHLH2 in the nodules gradually decreased from the meristematic zone to the nitrogen fixation zone, whereas the expression of MtCP77 showed enhancement. These results indicate that MtbHLH2 and MtCP77 have opposite functions in the regulation of nodule senescence. These results reveal significant roles for MtbHLH2 and MtCP77 in plant PCD, ROS accumulation, and nodule senescence, and improve our understanding of the regulation of the nodule senescence process.

Barley cysteine protease PAP14 plays a role in degradation of chloroplast proteins

Chloroplast protein degradation is known to occur both inside chloroplasts and in the vacuole. Genes encoding cysteine proteases have been found to be highly expressed during leaf senescence. However, it remains unclear where they participate in chloroplast protein degradation. In this study HvPAP14, which belongs to the C1A family of cysteine proteases, was identified in senescing barley (Hordeum vulgare L.) leaves by affinity enrichment using the mechanism-based probe DCG-04 targeting cysteine proteases and subsequent mass spectrometry. Biochemical analyses and expression of a HvPAP14:RFP fusion construct in barley protoplasts was used to identify the subcellular localization and putative substrates of HvPAP14. The HvPAP14:RFP fusion protein was detected in the endoplasmic reticulum and in vesicular bodies. Immunological studies showed that HvPAP14 was mainly located in chloroplasts, where it was found in tight association with thylakoid membranes. The recombinant enzyme was activated by low pH, in accordance with the detection of HvPAP14 in the thylakoid lumen. Overexpression of HvPAP14 in barley revealed that the protease can cleave LHCB proteins and PSBO as well as the large subunit of Rubisco. HvPAP14 is involved in the normal turnover of chloroplast proteins and may have a function in bulk protein degradation during leaf senescence.

Uncovering extensive post-translation regulation during human cell cycle progression by integrative multi-'omics analysis

BACKGROUND

Analysis of high-throughput multi-'omics interactions across the hierarchy of expression has wide interest in making inferences with regard to biological function and biomarker discovery. Expression levels across different scales are determined by robust synthesis, regulation and degradation processes, and hence transcript (mRNA) measurements made by microarray/RNA-Seq only show modest correlation with corresponding protein levels.

RESULTS

In this work we are interested in quantitative modelling of correlation across such gene products. Building on recent work, we develop computational models spanning transcript, translation and protein levels at different stages of the H. sapiens cell cycle. We enhance this analysis by incorporating 25+ sequence-derived features which are likely determinants of cellular protein concentration and quantitatively select for relevant features, producing a vast dataset with thousands of genes. We reveal insights into the complex interplay between expression levels across time, using machine learning methods to highlight outliers with respect to such models as proteins associated with post-translationally regulated modes of action.

CONCLUSIONS

We uncover quantitative separation between modified and degraded proteins that have roles in cell cycle regulation, chromatin remodelling and protein catabolism according to Gene Ontology; and highlight the opportunities for providing biological insights in future model systems.

The impact of photosynthesis on initiation of leaf senescence

Senescence is the last stage of leaf development preceding the death of the organ, and it is important for nutrient remobilization and for feeding sink tissues. There are many reports on leaf senescence, but the mechanisms initiating leaf senescence are still poorly understood. Leaf senescence is affected by many environmental factors and seems to vary in different species and even varieties of plants, which makes it difficult to generalize the mechanism. Here, we give an overview on studies reporting about alterations in the composition of the photosynthetic electron transport chain in chloroplasts during senescence. We hypothesize that alternative electron flow and related generation of the proton motive force required for ATP synthesis become increasingly important during progression of senescence. We address the generation of reactive oxygen species (ROS) in chloroplasts in the initiation of senescence, retrograde signaling from the chloroplast to the nucleus and ROS-dependent signaling associated with leaf senescence. Finally, a few ideas for increasing crop yields by increasing the chloroplast lifespan are presented.

Ubiquitin related enzymes and plant-specific ubiquitin ligase ATL family in tomato plants

Ubiquitination is one of the fundamental post-translational modifications of proteins with ubiquitin, a conserved 76-amino acid protein present in eukaryotes, which is catalyzed by ubiquitin ligase. Compared with humans, the number of ubiquitin ligase genes is nearly double in plant species such as Arabidopsis and rice, suggesting that this enzyme plays critical roles in many aspects of plant growth, including development and abiotic and biotic environmental stress responses. In addition to its fundamental activities in eukaryotic cells, ubiquitin signaling mediates plant specific cellular functions, including phytohormone response, seed and fruit development, and biotic and abiotic stress responses. The ATL family is a RING-H2 type ubiquitin ligase widely conserved in plant species. We previously showed that the plant specific ubiquitin ligase ATL31 regulates the carbon/nitrogen-nutrient response and pathogen resistance in Arabidopsis, and we identified and characterized the basic biochemical function of an ATL31 homologue in tomato plants (Solanum lycopersicum L.). This protein, called SlATL31, may act as a ubiquitin ligase in tomato fruit. The tomato is a major crop plant and a model system for fleshy fruit development. This review provides an overview of the ubiquitin ligases and related enzymes, and highlights the ubiquitin ligase ATL family in tomato plants.

Proteomic Analysis Reveals the Positive Effect of Exogenous Spermidine in Tomato Seedlings' Response to High-Temperature Stress

Polyamines are phytohormones that regulate plant growth and development as well as the response to environmental stresses. To evaluate their functions in high-temperature stress responses, the effects of exogenous spermidine (Spd) were determined in tomato leaves using two-dimensional electrophoresis and MALDI-TOF/TOF MS. A total of 67 differentially expressed proteins were identified in response to high-temperature stress and/or exogenous Spd, which were grouped into different categories according to biological processes. The four largest categories included proteins involved in photosynthesis (27%), cell rescue, and defense (24%), protein synthesis, folding and degradation (22%), and energy and metabolism (13%). Exogenous Spd up-regulated most identified proteins involved in photosynthesis, implying an enhancement in photosynthetic capacity. Meanwhile, physiological analysis showed that Spd could improve net photosynthetic rate and the biomass accumulation. Moreover, an increased high-temperature stress tolerance by exogenous Spd would contribute to the higher expressions of proteins involved in cell rescue and defense, and Spd regulated the antioxidant enzymes activities and related genes expression in tomato seedlings exposed to high temperature. Taken together, these findings provide a better understanding of the Spd-induced high-temperature resistance by proteomic approaches, providing valuable insight into improving the high-temperature stress tolerance in the global warming epoch.

Resonance assignments and secondary structure of a phytocystatin from Sesamum indicum

A cDNA encoding a cysteine protease inhibitor, cystatin was cloned from sesame (Sesamum indicum L.) seed. This clone was constructed into an expression vector and expressed in E. coli and purified to homogeneous. The recombinant sesame cystatin (SiCYS) showed effectively inhibitory activity toward C1 cysteine proteases. In order to unravel its inhibitory action from structural point of view, multidimensional heteronuclear NMR techniques were used to characterize the structure of SiCYS. The full (1)H, (15)N, and (13)C resonances of SiCYS were assigned. The secondary structure of SiCYS was identified by using the assigned chemical shifts of (1)H(α), (13)C(α), (13)C(β), and (13)CO through the consensus chemical shift index (CSI). The results of CSI analysis of SiCYS suggest eight β-strands (residues 33-46, 51-61, 63-75, 80-87, 150-155, 157-169, 172-183, and 192-195) and two α-helices (residues 16-30, and 120-135).

A triticale water-deficit-inducible phytocystatin inhibits endogenous cysteine proteinases in vitro

Water-deficit is accompanied by an increase in proteolysis. Phytocystatins are plant inhibitors of cysteine proteinases that belong to the papain and legumain family. A cDNA encoding the protein inhibitor TrcC-8 was identified in the vegetative organs of triticale. In response to water-deficit, increases in the mRNA levels of TrcC-8 were observed in leaf and root tissues. Immunoblot analysis indicated that accumulation of the TrcC-8 protein occurred after 72h of water-deficit in the seedlings. Using recombinant protein, inhibitory activity of TrcC-8 against cysteine proteases from triticale and wheat tissues was analyzed. Under water-deficit conditions, there are increases in cysteine proteinase activities in both plant tissues. The cysteine proteinase activities were inhibited by addition of the recombinant TrcC-8 protein. These results suggest a potential role for the triticale phytocystatin in modulating cysteine proteinase activities during water-deficit conditions.

Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages

Background

Prolyl oligopeptidases (POPs) are proteolytic enzymes, widely distributed in all the kingdoms of life. Bacterial POPs are pharmaceutically important enzymes, yet their functional and evolutionary details are not fully explored. Therefore, current analysis is aimed at understanding the distribution, domain architecture, probable biological functions and gene family expansion of POPs in bacterial and archaeal lineages.

Results

Exhaustive sequence analysis of 1,202 bacterial and 91 archaeal genomes revealed ~3,000 POP homologs, with only 638 annotated POPs. We observed wide distribution of POPs in all the analysed bacterial lineages. Phylogenetic analysis and co-clustering of POPs of different phyla suggested their common functions in all the prokaryotic species. Further, on the basis of unique sequence motifs we could classify bacterial POPs into eight subtypes. Analysis of coexisting domains in POPs highlighted their involvement in protein-protein interactions and cellular signaling. We proposed significant extension of this gene family by characterizing 39 new POPs and 158 new α/β hydrolase members.

Conclusions

Our study reflects diversity and functional importance of POPs in bacterial species. Many genomes with multiple POPs were identified with high sequence variations and different cellular localizations. Such anomalous distribution of POP genes in different bacterial genomes shows differential expansion of POP gene family primarily by multiple horizontal gene transfer events.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-985) contains supplementary material, which is available to authorized users.

Gel-based comparative phosphoproteomic analysis on rice embryo during germination

Seed germination is a well regulated process, which incorporates many events including signal transduction, mobilization of reserves, reactive oxygen species scavenging and cell division. Although many transcriptomic and proteomic studies have been conducted on this process, regulation of protein modification has not been studied. To better understand the mechanism, a gel-based comparative phosphoproteomic study was performed on rice embryo during the germination process. In total, 168 protein spots exhibited significantly changed Pro-Q staining intensity during germination. Using matrix-assisted laser deionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis, 193 proteins were identified. By combining Pro-Q and Coomassie brilliant blue stain intensity analyses, 109 proteins were verified to be phosphorylation regulation proteins. Functional analyses indicated that phosphorylation of proteins involved in stress response and storage was gradually enhanced. Phosphorylation of signal transduction proteins was mainly activated during the early stage of germination, while stress response and storage protein phosphorylation were enhanced at the late stage. Enzyme assays proved that the phosphorylation of fructokinase, pyruvate kinase, malate dehydrogenase, GDP-mannose 3,5-epimerase1, ascorbate peroxidase and glutathione S-transferase could consistently enhance their activity. This study showed the dynamic changes of protein phosphorylation status in rice embryo during germination and provided new insight into understanding the mechanism underlying this process.

Analysis of osmoadaptation system in budding yeast suggests that regulated degradation of glycerol synthesis enzyme is key to near-perfect adaptation

In order to maintain its turgor pressure at a desired homeostatic level, budding yeast, Saccharomyces cerevisiae responds to the external variation of the osmotic pressure by varying its internal osmotic pressure through regulation of synthesis and transport of the intracellular glycerol. Hog1PP (dually phosphorylated Hog1), a final effector in the signalling pathway of the hyper osmotic stress, regulates the glycerol synthesis both at transcriptional and non-transcriptional stages. It is known that for a step-change in salt concentration leading to moderate osmotic shock, Hog1PP activity shows a transient response before it returns to the vicinity of pre-stimulus level. It is believed that an integrating process in a negative feedback loop can be a design strategy to yield such an adaptive response. Several negative feedback loops have been identified in the osmoadaptation system in yeast. However, the precise location of the integrating process in the osmoadaptation system which includes signalling, gene regulation, metabolism and biophysical modules is unclear. To address this issue, we developed a reduced model which captures various experimental observations of the osmoadaptation behaviour of wild type and mutant strains. Dynamic simulations and steady state analysis suggested that known information about the osmoadaptation system of budding yeast does not necessarily give a perfect integrating process through the known feedback loops of Hog1PP. On the other hand, regulation of glycerol synthesising enzyme degradation can result in a near integrating process leading to a near-perfect adaptation.

Molecular Cloning, Expression, and Functional Characterization of a Cystatin from Pineapple Stem

A cDNA fragment encoding the cysteine protease inhibitor, cystatin, was cloned from pineapple (Ananas comosus) stem. This clone was constructed in a fusion vector and was easily over-expressed in Escherichia coli; satisfactory over-expression of non-fusion cystatin was achieved after an additional start codon was inserted prior to its coding sequence. Both recombinant cystatins were predominately found in the soluble fraction of the cell extract, and were demonstrated to be functionally active in a reverse zymographic assay. The fusion and non-fusion cystatins were separately purified to homogeneity via a His-tag or papain-coupling affinity column. Effective inhibitory activity against papain was detected with both the fusion and non-fusion cystatins with comparable K(i) values of 1.18 x 10(-10) M and 9.53 x 10(-11) M, respectively. The recombinant cystatins were found to be thermally stable up to 60 degrees C. Inhibition of the endogenous protease activity in minced fish muscle revealed that the recombinant pineapple cystatins might be an adequate stabilizer to prevent protein degradation during industrial food processing.

Silencing of the CaCP gene delays salt- and osmotic-induced leaf senescence in Capsicum annuum L

Cysteine proteinases have been known to participate in developmental processes and in response to stress in plants. Our present research reported that a novel CP gene, CaCP, was involved in leaf senescence in pepper (Capsicum annuum L.). The full-length CaCP cDNA is comprised of 1316 bp, contains 1044 nucleotides in open reading frame (ORF), and encodes a 347 amino acid protein. The deduced protein belongs to the papain-like cysteine proteases (CPs) superfamily, containing a highly conserved ERFNIN motif, a GCNGG motif and a conserved catalytic triad. This protein localized to the vacuole of plant cells. Real-time quantitative PCR analysis revealed that the expression level of CaCP gene was dramatically higher in leaves and flowers than that in roots, stems and fruits. Moreover, CaCP transcripts were induced upon during leaf senescence. CaCP expression was upregulated by plant hormones, especially salicylic acid. CaCP was also significantly induced by abiotic and biotic stress treatments, including high salinity, mannitol and Phytophthora capsici. Loss of function of CaCP using the virus-induced gene-silencing technique in pepper plants led to enhanced tolerance to salt- and osmotic-induced stress. Taken together, these results suggest that CaCP is a senescence-associated gene, which is involved in developmental senescence and regulates salt- and osmotic-induced leaf senescence in pepper.

Proteolysis of recombinant proteins in bioengineered plant cells

Plants are increasingly used as alternative expression hosts for the production of recombinant proteins offering many advantages including higher biomass and the ability to perform post-translational modifications on complex proteins. Key challenges for optimized accumulation of recombinant proteins in a plant system still remain, including endogenous plant proteolytic activity, which may severely compromise recombinant protein stability. Several strategies have recently been applied to improve protein stability by limiting protease action such as recombinant protein production in various sub-cellular compartments or application of protease inhibitors to limit protease action. A short update on the current strategies applied is provided here, with particular focus on sub-cellular sites previously selected for recombinant protein production and the co-expression of protease inhibitors to limit protease activity.

A novel aspartic acid protease gene from pineapple fruit (Ananas comosus): cloning, characterization and relation to postharvest chilling stress resistance

A full-length cDNA encoding a putative aspartic acid protease (AcAP1) was isolated for the first time from the flesh of pineapple (Ananas comosus) fruit. The deduced sequence of AcAP1 showed all the common features of a typical plant aspartic protease phytepsin precursor. Analysis of AcAP1 gene expression under postharvest chilling treatment in two pineapple varieties differing in their resistance to blackheart development revealed opposite trends. The resistant variety showed an up-regulation of AcAP1 precursor gene expression whereas the susceptible showed a down-regulation in response to postharvest chilling treatment. The same trend was observed regarding specific AP enzyme activity in both varieties. Taken together our results support the involvement of AcAP1 in postharvest chilling stress resistance in pineapple fruits.

Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes

MOTIVATION

Despite much dynamical cellular behaviour being achieved by accurate regulation of protein concentrations, messenger RNA abundances, measured by microarray technology, and more recently by deep sequencing techniques, are widely used as proxies for protein measurements. Although for some species and under some conditions, there is good correlation between transcriptome and proteome level measurements, such correlation is by no means universal due to post-transcriptional and post-translational regulation, both of which are highly prevalent in cells. Here, we seek to develop a data-driven machine learning approach to bridging the gap between these two levels of high-throughput omic measurements on Saccharomyces cerevisiae and deploy the model in a novel way to uncover mRNA-protein pairs that are candidates for post-translational regulation.

RESULTS

The application of feature selection by sparsity inducing regression (l₁ norm regularization) leads to a stable set of features: i.e. mRNA, ribosomal occupancy, ribosome density, tRNA adaptation index and codon bias while achieving a feature reduction from 37 to 5. A linear predictor used with these features is capable of predicting protein concentrations fairly accurately (R² = 0.86). Proteins whose concentration cannot be predicted accurately, taken as outliers with respect to the predictor, are shown to have annotation evidence of post-translational modification, significantly more than random subsets of similar size P < 0.02. In a data mining sense, this work also shows a wider point that outliers with respect to a learning method can carry meaningful information about a problem domain.

DREB2C acts as a transcriptional activator of the thermo tolerance-related phytocystatin 4 (AtCYS4) gene

Phytocystatins are proteinaceous inhibitors of cysteine proteases. They have been implicated in the regulation of plant protein turnover and in defense against pathogens and insects. Here, we have characterized an Arabidopsis phytocystatin family gene, Arabidopsis thaliana phytocystatin 4 (AtCYS4). AtCYS4 was induced by heat stress. The heat shock tolerance of AtCYS4-overexpressing transgenic plants was greater than that of wild-type and cys4 knock-down plants, as measured by fresh weight and root length. Although no heat shock elements were identified in the 5'-flanking region of the AtCYS4 gene, canonical ABA-responsive elements (ABREs) and dehydration-responsive elements (DREs) were found. Transient promoter activity measurements showed that AtCYS4 expression was up-regulated in unstressed protoplasts by co-expression of DRE-binding factor 2s (DREB2s), especially by DREB2C, but not by bZIP transcription factors that bind to ABREs (ABFs, ABI5 and AREBs). DREB2C bound to and activated transcription from the two DREs on the AtCYS4 promoter although some preference was observed for the GCCGAC DRE element over the ACCGAC element. AtCYS4 transcript and protein levels were elevated in transgenic DREB2C overexpression lines with corresponding decline of endogenous cysteine peptidase activity. We propose that AtCYS4 functions in thermotolerance under the control of the DREB2C cascade.

Microarray analysis of gene expression profiles in ripening pineapple fruits

BACKGROUND

Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening.

RESULTS

Microarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested.

CONCLUSIONS

This is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit ripening and non-climacteric fruit ripening in general.

Comparative proteomic analysis of early somatic and zygotic embryogenesis in Theobroma cacao L

Somatic embryogenesis can efficiently foster the propagation of Theobroma cacao, but the poor quality of resulted plantlet hinders the use of this technique in the commercial scale. The current study has been initiated to systematically compare the physiological mechanisms underlying somatic and zygotic embryogenesis in T. cacao on the proteome level. About 1000 protein spots per fraction could be separated by two-dimensional isoelectric focusing/SDS PAGE. More than 50 of the protein spots clearly differed in abundance between zygotic and somatic embryos: 33 proteins spots were at least 3-fold higher in abundance in zygotic embryos and 20 in somatic embryos. Analyses of these protein spots differing in volume by mass spectrometry resulted in the identification of 68 distinct proteins. Many of the identified proteins are involved in genetic information processing (21 proteins), carbohydrate metabolism (11 proteins) and stress response (7 proteins). Somatic embryos especially displayed many stress related proteins, few enzymes involved in storage compound synthesis and an exceptional high abundance of endopeptidase inhibitors. Phosphoenolpyruvate carboxylase, which was accumulated more than 3-fold higher in zygotic embryos, represents a prominent enzyme in the storage compound metabolism in cacao seeds. Implications on the improvement of somatic embryogenesis in cacao are discussed.

Solution structure of a phytocystatin from Ananas comosus and its molecular interaction with papain

The structure of a recombinant pineapple cystatin (AcCYS) was determined by NMR with the RMSD of backbone and heavy atoms of twenty lowest energy structures of 0.56 and 1.11 Å, respectively. It reveals an unstructured N-terminal extension and a compact inhibitory domain comprising a four-stranded antiparallel β-sheet wrapped around a central α-helix. The three structural motifs (G(45), Q(89)XVXG, and W(120)) putatively responsible for the interaction with papain-like proteases are located in one side of AcCYS. Significant chemical shift perturbations in two loop regions, residues 45 to 48 (GIYD) and residues 89 to 91 (QVV), of AcCYS strongly suggest their involvement in the binding to papain, consistent with studies on other members of the cystatin family. However, the highly conserved W120 appears not to be involved in the binding with papain as no chemical shift perturbation was observed. Chemical shift index analysis further indicates that the length of the α-helix is shortened upon association with papain. Collectively, our data suggest that AcCYS undergoes local secondary structural rearrangements when papain is brought into close contact. A molecular model of AcCYS/papain complex is proposed to illustrate the interaction between AcCYS and papain, indicating a complete blockade of the catalytic triad by AcCYS.

Use of transgenic oryzacystatin-I-expressing plants enhances recombinant protein production

Plants are an effective and inexpensive host for the production of commercially interesting heterologous recombinant proteins. The Escherichia coli-derived glutathione reductase was transiently expressed as a recombinant model protein in the cytosol of tobacco plants using the technique of leaf agro-infiltration. Proteolytic cysteine protease activity progressively increased over time when glutathione reductase accumulated in leaves. Application of cysteine protease promoter-GUS fusions in transgenic tobacco identified a cysteine protease NtCP2 expressed in mature leaves and being stress responsive to be expressed as a consequence of agro-infiltration. Transgenic tobacco plants constitutively expressing the rice cysteine protease inhibitor oryzacystatin-I had significantly lower cysteine protease activity when compared to non-transgenic tobacco plants. Lower cysteine protease activity in transgenic plants was directly related to higher glutathione reductase activity and also higher glutathione reductase amounts in transgenic plants. Overall, our work has demonstrated as a novel aspect that transgenic tobacco plants constitutively expressing an exogenous cysteine protease inhibitor have the potential for producing more recombinant protein which is very likely due to the reduced activity of endogenous cysteine protease.

Proteolytic activities in Phaseolus vulgaris cotyledons under copper stress

The changes in the protease activities of bean cotyledons were investigated in response to copper stress. Assays using synthetic substrates and specific protease inhibitors followed by activity measurements and electrophoresis analysis allowed to study the classes of enzymes involved in the storage protein mobilization during the germination of bean (Phaseolus vulgaris L) seeds, and then identify which ones were affected in the presence of 200 μM CuCl2 in the imbibition medium. Copper treatment affected embryo growth and total protease activity. The results of SDS-gelatin-PAGE show that Cu excess led to a decrease in protease activity of 45 to 66 kDa. Moreover, cysteine-, aspartic- and metallo-protease activities were markedly lowered under copper stress, while serine-protease one was enhanced as well as its activity dependent abundance in comparison with control. However, the relative distribution of major cysteine protease in H2O-germinated seeds was significantly diminished after Cu exposure. Thus, copper excess can disturb the nitrogen freeing from reserve tissues at enzymatic level; differential responses of protease classes are discussed, notably, cysteine protease in the way of storage protein mobilization and serine protease in protective mechanism one.

Biochemical and biophysical changes associated with magnetopriming in germinating cucumber seeds

Seeds of cucumber were exposed to static magnetic field strength from 100 to 250 mT for 1, 2 or 3 h. Germination-percentage, rate of germination, length of seedling and dry weight increased by 18.5, 49, 34 and 33% respectively in magnetoprimed seeds compared to unexposed seeds. Among different magnetic field doses, 200 mT for 1 h showed significant effect on germination parameters and hence selected for studying changes in water uptake, (1)H transverse relaxation time (T(2)), hydrolytic enzymes, reactive oxygen species and antioxidant enzyme system in germinating seeds. Water uptake and T(2) values were significantly higher in treated seeds during imbibition. The activities of hydrolytic enzymes, amylase and protease were greater than the untreated controls by 51% and 13% respectively. Superoxide radicals also enhanced by 40% and hydrogen peroxide by 8% in magnetically exposed seeds. In magetoprimed seeds, increased activities of antioxidant enzymes, superoxide dismutase (8%), catalase (83%) and glutathione reductase (77%) over control was recorded. We report that magnetopriming of dry seeds can be effectively used as a pre-sowing treatment for seed invigoration in cucumber. Unlike other priming treatments seed is not required to be dehydrated after priming, allowing easy storage.

Sequential posttranslational modifications program FEN1 degradation during cell-cycle progression

We propose that cell-cycle-dependent timing of FEN1 nuclease activity is essential for cell-cycle progression and the maintenance of genome stability. After DNA replication is complete at the exit point of the S phase, removal of excess FEN1 may be crucial. Here, we report a mechanism that controls the programmed degradation of FEN1 via a sequential cascade of posttranslational modifications. We found that FEN1 phosphorylation stimulated its SUMOylation, which in turn stimulated its ubiquitination and ultimately led to its degradation via the proteasome pathway. Mutations or inhibitors that blocked the modification at any step in this pathway suppressed FEN1 degradation. Critically, the presence of SUMOylation- or ubiquitination-defective, nondegradable FEN1 mutant protein caused accumulation of Cyclin B, delays in the G1 and G2/M phases, and polyploidy. These findings may represent a newly identified regulatory mechanism used by cells to ensure precise cell-cycle progression and to prevent transformation.

Subtilases - versatile tools for protein turnover, plant development, and interactions with the environment

Subtilases (SBTs) constitute a large family of serine peptidases. They are commonly found in Archaea, Bacteria and Eukarya, with many more SBTs in plants as compared to other organisms. The expansion of the SBT family in plants was accompanied by functional diversification, and novel, plant-specific physiological roles were acquired in the course of evolution. In addition to their contribution to general protein turnover, plant SBTs are involved in the development of seeds and fruits, the manipulation of the cell wall, the processing of peptide growth factors, epidermal development and pattern formation, plant responses to their biotic and abiotic environment, and in programmed cell death. Plant SBTs share many properties with their bacterial and mammalian homologs, but the adoption of specific roles in plant physiology is also reflected in the acquisition of unique biochemical and structural features that distinguish SBTs in plants from those in other organisms. In this article we provide an overview of the earlier literature on the discovery of the first SBTs in plants, and highlight recent findings with respect to their physiological relevance, structure and function.

Root carbon and protein metabolism associated with heat tolerance

Extensive past efforts have been taken toward understanding heat tolerance mechanisms of the aboveground organs. Root systems play critical roles in whole-plant adaptation to heat stress, but are less studied. This review discusses recent research results revealing some critical physiological and metabolic factors underlying root thermotolerance, with a focus on temperate perennial grass species. Comparative analysis of differential root responses to supraoptimal temperatures by a heat-adapted temperate C3 species, Agrostis scabra, which can survive high soil temperatures up to 45 °C in geothermal areas in Yellow Stone National Park, and a heat-sensitive cogeneric species, Agrostis stolonifera, suggested that efficient carbon and protein metabolism is critical for root thermotolerance. Superior root thermotolerance in a perennial grass was associated with a greater capacity to control respiratory costs through respiratory acclimation, lowering carbon investment in maintenance for protein turnover, and efficiently partitioning carbon into different metabolic pools and alternative respiration pathways. Proteomic analysis demonstrated that root thermotolerance was associated with an increased maintenance of stability and less degradation of proteins, particularly those important for metabolism and energy production. In addition, thermotolerant roots are better able to maintain growth and activity during heat stress by activating stress defence proteins such as those participating in antioxidant defence (i.e. superoxide dismutase, peroxidase, glutathione S-transferase) and chaperoning protection (i.e. heat shock protein).

Resonance assignments and secondary structure of a phytocystatin from Ananas comosus

A cDNA encoding a cysteine protease inhibitor, cystatin was cloned from pineapple (Ananas comosus L.) stem. This clone was constructed into an expression vector and expressed in E. coli and purified to homogeneous. The recombinant pineapple cystatins (AcCYS) showed effectively inhibitory activity toward cysteine proteases including papain, bromelain, and cathepsin B. In order to unravel its inhibitory action from structural point of view, multidimensional heteronuclear NMR techniques were used to characterize the structure of AcCYS. The full (1)H, (15)N, and (13)C resonance assignments of AcCYS were determined. The secondary structure of AcCYS was identified by using the assigned chemical shift of (1)Hα, (13)Cα, (13)Cβ, and (13)CO through the consensus chemical shift index (CSI). The results of CSI analysis suggest 5 β-strands (residues 45-47, 84-91, 94-104, 106-117, and 123-130) and one α-helix (residues 55-73).

Release of apical dominance in potato tuber is accompanied by programmed cell death in the apical bud meristem

Potato (Solanum tuberosum) tuber, a swollen underground stem, is used as a model system for the study of dormancy release and sprouting. Natural dormancy release, at room temperature, is initiated by tuber apical bud meristem (TAB-meristem) sprouting characterized by apical dominance (AD). Dormancy is shortened by treatments such as bromoethane (BE), which mimics the phenotype of dormancy release in cold storage by inducing early sprouting of several buds simultaneously. We studied the mechanisms governing TAB-meristem dominance release. TAB-meristem decapitation resulted in the development of increasing numbers of axillary buds with time in storage, suggesting the need for autonomous dormancy release of each bud prior to control by the apical bud. Hallmarks of programmed cell death (PCD) were identified in the TAB-meristems during normal growth, and these were more extensive when AD was lost following either extended cold storage or BE treatment. Hallmarks included DNA fragmentation, induced gene expression of vacuolar processing enzyme1 (VPE1), and elevated VPE activity. VPE1 protein was semipurified from BE-treated apical buds, and its endogenous activity was fully inhibited by a cysteinyl aspartate-specific protease-1-specific inhibitor N-Acetyl-Tyr-Val-Ala-Asp-CHO (Ac-YVAD-CHO). Transmission electron microscopy further revealed PCD-related structural alterations in the TAB-meristem of BE-treated tubers: a knob-like body in the vacuole, development of cytoplasmic vesicles, and budding-like nuclear segmentations. Treatment of tubers with BE and then VPE inhibitor induced faster growth and recovered AD in detached and nondetached apical buds, respectively. We hypothesize that PCD occurrence is associated with the weakening of tuber AD, allowing early sprouting of mature lateral buds.

Measuring intracellular hsp70 in leukocytes by flow cytometry

Heat shock or stress proteins are constitutively expressed redox-sensitive proteins, the synthesis of which is induced in almost all organisms exposed to a range of stressors, including heat shock, oxidative stress, free radicals, UV radiation, and heavy metals. This unit details a method, with supporting protocols, for the measurement of their expression in peripheral blood leukocytes by flow cytometry.

The Arabidopsis multistress regulator TSPO is a heme binding membrane protein and a potential scavenger of porphyrins via an autophagy-dependent degradation mechanism

TSPO, a stress-induced, posttranslationally regulated, early secretory pathway-localized plant cell membrane protein, belongs to the TspO/MBR family of regulatory proteins, which can bind porphyrins. This work finds that boosting tetrapyrrole biosynthesis enhanced TSPO degradation in Arabidopsis thaliana and that TSPO could bind heme in vitro and in vivo. This binding required the His residue at position 91 (H91), but not that at position 115 (H115). The H91A and double H91A/H115A substitutions stabilized TSPO and rendered the protein insensitive to heme-regulated degradation, suggesting that heme binding regulates At-TSPO degradation. TSPO degradation was inhibited in the autophagy-defective atg5 mutant and was sensitive to inhibitors of type III phosphoinositide 3-kinases, which regulate autophagy in eukaryotic cells. Mutation of the two Tyr residues in a putative ubiquitin-like ATG8 interacting motif of At-TSPO did not affect heme binding in vitro but stabilized the protein in vivo, suggesting that downregulation of At-TSPO requires an active autophagy pathway, in addition to heme. Abscisic acid-dependent TSPO induction was accompanied by an increase in unbound heme levels, and downregulation of TSPO coincided with the return to steady state levels of unbound heme, suggesting that a physiological consequence of active TSPO downregulation may be heme scavenging. In addition, overexpression of TSPO attenuated aminolevulinic acid-induced porphyria in plant cells. Taken together, these data support a role for TSPO in porphyrin binding and scavenging during stress in plants.

Acclimation to frost alters proteolytic response of wheat seedlings to drought

A comparative examination of cysteine proteinases in winter wheat (Triticum aestivum L.) seedlings differing in sensitivity to frost and drought revealed many similarities and differences in response to water deprivation. Azocaseinolytic activity was enhanced under water deficiency, but the enhancement was significantly lower in the tolerant genotype (Kobra cultivar). On the contrary, acclimation of wheat seedlings at low temperature had no effect on the proteolytic activity of the tolerant cultivar and depressed the azocaseinolytic activity of the sensitive cultivar (Tortija). However, the observed depression of enzyme activity was fully reversible under dehydration. The content of soluble proteins was reduced in dehydrated non-acclimated and in acclimated seedlings of the frost-sensitive cultivar, but increased in acclimated seedlings of the tolerant cultivar. The cysteine proteinases were preferentially induced under water deficiency when assessment was based on the inhibitory effect of iodoacetate on azocasein hydrolysis. Separation of cysteine proteinases by SDS-PAGE containing gelatin as a substrate showed two bands with apparent molecular masses of 36 and 38 kDa in the sensitive cultivar, and a third band was detected (42 kDa) in the resistant cultivar. Water deficit and low temperature induced the new cysteine proteinases of molecular masses about 29, 33 and 42 kDa in sensitive non-acclimated seedlings. Polyclonal antibodies raised against Arabidopsis proteinase responsive to drought (RD21) cross-reacted with the protein in the 33 kDa region, and a slight signal was obtained in the 42 kDa region, but only in dehydrated seedlings acclimated to frost. Several polypeptides of molecular masses of 30, 22, 20 and 18 kDa were recognized by the Arabidopsis aleurain-like proteinase (AtALEU) antibodies. The results presented indicate that cysteine proteinases are potentially responsible for both low temperature and drought tolerance.

Recombinant protease inhibitors for herbivore pest control: a multitrophic perspective

Protease inhibitors are a promising complement to Bt toxins for the development of insect-resistant transgenic crops, but their limited specificity against proteolytic enzymes and the ubiquity of protease-dependent processes in living organisms raise questions about their eventual non-target effects in agroecosystems. After a brief overview of the main factors driving the impacts of insect-resistant transgenic crops on non-target organisms, the possible effects of protease inhibitors are discussed from a multitrophic perspective, taking into account not only the target herbivore proteases but also the proteases of other organisms found along the trophic chain, including the plant itself. Major progress has been achieved in recent years towards the design of highly potent broad-spectrum inhibitors and the field deployment of protease inhibitor-expressing transgenic plants resistant to major herbivore pests. A thorough assessment of the current literature suggests that, whereas the non-specific inhibitory effects of recombinant protease inhibitors in plant food webs could often be negligible and their 'unintended' pleiotropic effects in planta of potential agronomic value, the innocuity of these proteins might always remain an issue to be assessed empirically, on a case-by-case basis.

Production of heterologous proteins in plants: strategies for optimal expression

Plants are a promising expression system for the production of heterologous proteins, especially therapeutic proteins. Currently the majority of therapeutic proteins are produced in mammalian cell lines or bacteria. In a few cases insects, yeast and fungi have been developed for production of human proteins. However, these expression systems have limitations in terms of suitability, cost, scalability, purification and post-translational modifications. Therefore, alternative expression systems are being developed in transgenic animals and transgenic plants. Transgenic plants could provide an attractive alternative in terms of low production cost and lower capital investment in infrastructure, and with appropriate post-translational modifications. The potential of plants as an expression host has not been capitalized, primarily due to lower level of expression of transgenes in plants. The present review will evaluate the rate limiting steps of plant expression systems and suggest strategies to optimize protein expression at each of the steps: gene integration, transcription, translation and protein accumulation.

Effect on germination and early growth characteristics in sunflower (Helianthus annuus) seeds exposed to static magnetic field

Seeds of sunflower (Helianthus annuus) were exposed in batches to static magnetic fields of strength from 0 to 250mT in steps of 50mT for 1-4h in steps of 1h. Treatment of sunflower seeds in these magnetic fields increased the speed of germination, seedling length and seedling dry weight under laboratory germination tests. Of the various treatments, 50 and 200mT for 2h yielded the peak performance. Exposure of seeds to magnetic fields improved seed coat membrane integrity and reduced the cellular leakage and electrical conductivity. Treated seeds planted in soil resulted in statistically higher seedling dry weight, root length, root surface area and root volume in 1-month-old seedlings. In germinating seeds, enzyme activities of alpha-amylase, dehydrogenase and protease were significantly higher in treated seeds in contrast to controls. The higher enzyme activity in magnetic-field-treated sunflower seeds could be triggering the fast germination and early vigor of seedlings.

Two-dimensional gel electrophoretic protein profile analysis during seed development of Ocotea catharinensis: a recalcitrant seed species

The aim of the present work was to characterize changes in the protein profile throughout seed development in O. catharinensis, a recalcitrant species, by two-dimensional gel electrophoresis. Protein extraction was undertaken by using a thiourea/urea buffer, followed by a precipitation step with 10% TCA. Comparative analysis during seed development showed that a large number of proteins were exclusively detected in each developmental stage. The cotyledonary stage, which represents the transition phase between embryogenesis and the beginning of metabolism related to maturation, presents the highest number of stage-specific spots. Protein identification, through MS/MS analysis, resulted in the identification of proteins mainly related to oxidative metabolism and storage synthesis. These findings contribute to a better understanding of protein metabolism during seed development in recalcitrant seeds, besides providing information on established markers that could be useful in defining and improving somatic embryogenesis protocols, besides monitoring the development of somatic embryos in this species.

Crystallization and preliminary X-ray analysis of carnein, a serine protease from Ipomoea carnea

Carnein is an 80 kDa subtilisin-like serine protease from the latex of the plant Ipomoea carnea which displays an exceptional resistance to chemical and thermal denaturation. In order to obtain the first crystal structure of a plant subtilisin and to gain insight into the structural determinants underlying its remarkable stability, carnein was isolated from I. carnea latex, purified and crystallized by the hanging-drop vapour-diffusion method. A data set was collected to 2.0 A resolution in-house from a single crystal at 110 K. The crystals belonged to the trigonal space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 126.9, c = 84.6 A, alpha = beta = 90, gamma = 120 degrees. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient is 2.46 A(3) Da(-1), corresponding to a solvent content of 50%. Structure determination of the enzyme is in progress.

Constitutive expression of a trypsin protease inhibitor confers multiple stress tolerance in transgenic tobacco

Protease inhibitors have been reported to confer insect resistance in transgenic plants, except for a rice protease inhibitor that conferred drought tolerance in transgenic rice plants. We have cloned a protease inhibitor of tobacco that is expressed under treatment with ABA, hydrogen peroxide, methyl jasmonate and wounding. The cDNA codes for a six-domain serine protease inhibitor with a deduced sequence of 396 amino acids. We have generated transgenic tobacco plants expressing the protease inhibitor constitutively under the 35S promoter. When analyzed in the T(2) generation, these transgenic plants exhibited tolerance to sodium chloride, variable pH and sorbitol, together with the expected resistance to the insect pests Spodoptera litura and Helicoverpa armigera. The transgenic plants showed enhanced seed germination, root length and root-shoot ratio, significantly enhanced total chlorophyll content and reduced thiobarbituric acid-reactive substances under stress. Under sodium chloride treatment, the transgenic plants have enhanced protease inhibitor activity. The transgenic plants exhibited a higher potassium content and an optimum Na+/K+ ratio. To our knowledge, this is the first report of transgenic plants with constitutive protease inhibitor expression showing tolerance to a wide range variable pH in the culture medium along with other stresses.

Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes

Background

Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms.

Results

A total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques. Phylogenetic analysis reveals several species-specific clusters of serine proteases suggesting their possible involvement in organism-specific functions. Atypical phylogenetic associations suggest an important role for lateral gene transfer events in facilitating the widespread distribution of the serine proteases in the prokaryotes. Domain organisations of the gene products were analysed, employing sensitive sequence search methods, to infer their probable biological functions. Trypsin, subtilisin and Lon protease families account for a significant proportion of the multi-domain representatives, while the D-Ala-D-Ala carboxypeptidase and the Clp protease families are mostly single-domain polypeptides in prokaryotes. Regulatory domains for protein interaction, signalling, pathogenesis, cell adhesion etc. were found tethered to the serine protease domains. Some domain combinations (such as S1-PDZ; LON-AAA-S16 etc.) were found to be widespread in the prokaryotic lineages suggesting a critical role in prokaryotes.

Conclusion

Domain architectures of many serine proteases and their homologues identified in prokaryotes are very different from those observed in eukaryotes, suggesting distinct roles for serine proteases in prokaryotes. Many domain combinations were found unique to specific prokaryotic species, suggesting functional specialisation in various cellular and physiological processes.

Identification and characterization of proteins associated with plant tolerance to heat stress

Heat stress is a major abiotic stress limiting plant growth and productivity in many areas of the world. Understanding mechanisms of plant adaptation to heat stress would facilitate the development of heat-tolerant cultivars for improving productivity in warm climatic regions. Protein metabolism involving protein synthesis and degradation is one of the most sensitive processes to heat stress. Changes in the level and expression pattern of some proteins may play an important role in plant adaptation to heat stress. The identification of stress-responsive proteins and pathways has been facilitated by an increasing number of tools and resources, including two-dimensional electrophoresis and mass spectrometry, and the rapidly expanding nucleotide and amino acid sequence databases. Heat stress may induce or enhance protein expression or cause protein degradation. The induction of heat-responsive proteins, particularly heat shock proteins (HSPs), plays a key role in plant tolerance to heat stress. Protein degradation involving various proteases is also important in regulating plant responses to heat stress. This review provides an overview of recent research on proteomic profiling for the identification of heat-responsive proteins associated with heat tolerance, heat induction and characteristics of HSPs, and protein degradation in relation to plant responses to heat stress.