Current Protein and Peptide Science - Volume 12, Issue 2, 2011

The roles of proteins in cells and organisms have always been the subject of intense research. The advent of proteomic techniques and the full exploitation of genomic and advanced biophysical approaches has accelerated protein research and increased our understanding of interactions and crosstalk among individual proteins and whole pathways. This issue presents a window on current plant protein research in directions which are essential for understanding the life and development of plants and at the same time represent hot topics for protein research today. Proteins are not only the ultimate products of genetic information, but also important guardians of chromosome stability. This is nicely demonstrated in the article by Peska et al., which reviews the role of proteins at chromosome termini, the telomeres, and focuses specifically on a group of double-strand DNA binding proteins possessing telobox, a Myb-related DNA-binding domain. The authors present telobox as a convenient motif for searching for telomere-binding proteins, but they emphasize pertinently the necessity of further critical evaluation of their true telomeric role. Interestingly, based on the presence of telobox motif, a putative telomeric protein in C. parqui, a plant species lacking canonical telomeric sequences, is reported. A related review by Amiard et al. starts where the previous one ends. Beginning with a brief introduction to telomeric proteins, it provides a succinct overview of recent advances in understanding the role of proteins in DNA damage response and shows how proteins involved in DNA damage response and repair not only contribute to the recognition of telomere dysfunction, but surprisingly, are directly implicated in telomere homeostasis itself....

Telobox is a Myb-related DNA-binding domain which is present in a number of yeast, plant and animal proteins. Its capacity to bind preferentially double-stranded telomeric DNA has been used in numerous studies to search for candidate telomeric proteins in various organisms, including plants. Here we provide an overview of these studies with a special emphasis on plants, where a specific subfamily of the proteins possessing the N-terminally positioned telobox is present in addition to more common C-terminal telobox proteins. We further demonstrate the presence of a telobox protein (CpTBP1) in Cestrum parqui, a plant lacking typical telomeres and telomerase. The protein shows nuclear localisation and association with chromatin. The role of this protein in ancestral and current telomere structure is discussed in the evolutionary context. Altogether, the present overview shows the importance of the telobox domain in a search for candidate telomere proteins but at the same time warns against oversimplified identification of any telobox protein with telomere structure without appropriate evidence of its telomeric localisation and function.

Repair of DNA damage is essential for the maintenance of the integrity and transmission of the genome in development and reproduction. Telomeres are nucleoprotein structures which protect the ends of (linear) eukaryotic chromosomes. Telomere dysfunction results in loss of this protection and the telomeres being recognised as DNA damage by the cellular DNA Damage Repair and Response (DDR) machinery, leading to senescence or cell death. Telomeric homeostasis is thus tightly controlled and many specific and non-specific proteins are involved in its regulation. Among these, DNA damage and Repair proteins contribute both to the recognition of telomere dysfunction and more surprisingly, are directly implicated in telomere homeostasis itself. Plants offer a great opportunity to study these mechanisms due to the fact that many key DNA repair and recombination proteins are non-essential in plants, in contrast to vertebrates. In the following text, after a brief summary of the current state of knowledge on telomere-specific proteins in plants, we review the DDR processes and the related proteins implicated in plant telomere stability. We focus specifically on telomere signalling and on recombination events induced by unprotected telomeres, at the origin of genome rearrangements and instability when telomere function is affected.

Cohesin complexes are critical for holding sister chromatids together during nuclear division. They also play important roles in the compaction of chromosomes and their bipolar attachment to the spindle, DNA double strand break repair, and the regulation of gene expression. Studies on sister chromatid cohesion in a wide range of organisms have shown that the proteins involved, and the general events of this important process are conserved between yeast, plants and animals. However, species-specific differences have been identified. In this review a general overview of cohesins, their roles-and mechanisms of action is presented, followed by a review of our current state of knowledge on plant cohesins. While plants utilize the same general set of cohesin proteins and similar processes to establish and release sister chromatid cohesion, they also exhibit a number of unique features that are likely to provide interesting new insights into the roles of these important proteins.

Chromosome stability is conditioned by functional chromatin structure of chromosome ends - telomeres. Organisation and regulation of telomere maintenance represent a complex process whose details still remain enigmatic, especially in plants. Several telomere-binding or telomere-associated proteins and distinct epigenetic marks have been shown to influence telomere length and telomerase activity. HMGB proteins play important role in dynamic changes of chromatin structure and are involved in regulation of cellular processes of key importance, such as replication, transcription, recombination and DNA-repair. HMGB proteins in plants are more diversified than in other eukaryotes. Here, we summarise the roles of plant HMGB proteins in regulation of chromatin structure and dynamics and report on the newly identified role of AtHMGB1 protein in the regulation of plant telomere length. Astonishingly, contrary to mice mHMGB1 homologue, AtHMGB1 does not affect telomerase activity and AtHMGB1 loss or overexpression does not cause any obvious changes in chromatin architecture.

Protein phosphorylation constitutes a major type of post-translational modifications mobilizing a high number of genes. It is involved in many crucial cell processes and largely participates in the features of the proteome. For several biological and technical reasons, the characterization of protein phosphorylation requires a combination of distinct procedures. In this review, a special emphasis is given to analytical strategies connected with the determination of the presence of phosphorylation sites and their localization by mass spectrometry (MS). The feasibility of selected combinations of analytical approaches for diverse objectives of phosphoproteomic research is discussed.

Multistep phosphorelay (MSP) pathways mediate a wide spectrum of adaptive responses in plants, including hormonal and abiotic stress regulations. Recent genetic evidence suggests both partial redundancy and possible functional cross-talk on the one hand and a certain level of specificity on the other. Here, we discuss recent achievements improving our understanding of possible molecular mechanisms of specificity in MSP. We consider a certain evolutionary conservation of ancestral two-component signalling systems from bacteria in a process of molecular recognition that, as we have recently shown, could be applied also to a certain extent in the case of plant MSP. Furthermore, we discuss possible roles of kinase and phosphatase activities, kinetics of both these enzymatic reactions, and phosphorylation lifetime. We include also recent findings on the expression specificity of individual members of MSP pathways and, finally, based on our recent findings, we speculate about a possible role of magnesium in regulation of MSP pathways in plants. All these mechanisms could significantly influence specificity and signalling output of the MSP pathways.

Auxin and cytokinins have been identified as key regulators of plant development. Recently, these phytohormones have been shown to interact during important developmental processes, including positioning, identity acquisition and maintenance of meristem organizing centres, regulation of balance between cell division and differentiation, and postembryonic de novo organogenesis. Here, we discuss recent advances in our understanding of the underlying molecular mechanisms at the levels of regulating metabolism, signalling, gene expression and protein stability.

Current models of the plasma membrane (PM) organization focus on the lateral heterogeneity of the membrane and its relation to the cell function. Increasing evidence in mammals and yeast supports the direct relationship between PM lateral microdomains and specific cell processes and functions (nutrient transport, signaling, protein and lipid sorting, endocytosis, pathogen entry etc.). However, for the present the functional significance of an enrichment of specific proteins and possibly lipids in plant PM domains as well as the underlying molecular mechanism driving the lateral PM segregation remain unaddressed. Here we summarize recent findings on the plant PM organization and its role in signaling pathways, with the special emphasis on auxin transport.

Actinorhizal symbioses are mutualistic associations between plants belonging to eight angiosperm families and soil bacteria of the genus Frankia. These interactions lead to the formation of new root organs, actinorhizal nodules, where the bacteria are hosted and fix atmospheric nitrogen thus providing the plant with an almost unlimited source of nitrogen for its nutrition. It involves an elaborate signaling between both partners of the symbiosis. In recent years, our knowledge of this signaling pathway has increased tremendously thanks to a series of technical breakthroughs including the sequencing of three Frankia genomes [1] and the implementation of RNA silencing technology for two actinorhizal species. In this review, we describe all these recent advances, current researches on symbiotic signaling in actinorhizal symbioses and give some potential future research directions.