Large accumulation of mRNA and DNA point modifications in a plant senescent tissue

Somatic Mutation and Evolution in Plants

Somatic mutations are common in plants, and they may accumulate and be passed on to gametes. The determinants of somatic mutation accumulation include the intraorganismal selective effect of mutations, the number of cell divisions that separate the zygote from the formation of gametes, and shoot apical meristem structure and branching. Somatic mutations can promote the evolution of diploidy, polyploidy, sexual recombination, outcrossing, clonality, and separate sexes, and they may contribute genetic variability in many other traits. The amplification of beneficial mutations via intraorganismal selection may relax selection to reduce the genomic mutation rate or to protect the germline in plants. The total rate of somatic mutation, the distribution of selective effects and fates in the plant body, and the degree to which the germline is sheltered from somatic mutations are still poorly understood. Our knowledge can be improved through empirical estimates of mutation rates and effects on cell lineages and whole organisms, such as estimates of the reduction in fitness of progeny produced by within- versus between-flower crosses on the same plant, mutation coalescent studies within the canopy, and incorporation of somatic mutation into theoretical models of plant evolutionary genetics.

Age-associated alterations in the somatic mutation and DNA methylation levels in plants

Somatic mutations of the nuclear and mitochondrial DNA and alterations in DNA methylation levels in mammals are well known to play important roles in ageing and various diseases, yet their specific contributions await further investigation. For plants, it has also been proposed that unrepaired DNA damage and DNA polymerase errors accumulate in plant cells and lead to increased somatic mutation rate and alterations in transcription, which eventually contribute to plant ageing. A number of studies also show that DNA methylation levels vary depending on the age of plant tissue and chronological age of a whole plant. Recent studies reveal that prolonged cultivation of plant cells in vitro induces single nucleotide substitutions and increases global DNA methylation level in a time-dependent fashion. Changes in DNA methylation are known to influence DNA repair and can lead to altered mutation rates, and, therefore, it is interesting to investigate both the genetic and epigenetic integrity in relationship to ageing in plants. This review will summarise and discuss the current studies investigating somatic DNA mutation and DNA methylation levels in relation to plant ageing and senescence. The analysis has shown that there still remains a lack of clarity concerning plant biological ageing and the role of the genetic and epigenetic instabilities in this process.

Ageing of trees: application of general ageing theories

The main questions posed in ageing theories are how ageing evolved and whether or not it is programmed. While these questions have not yet been clearly resolved, several groups of possible theories have been published on this topic. However, most of these theories do not consider plants, and the specific traits involved in their ageing mechanisms. The first trait covers clonality and sectoriality and the second concerns the lack of a differentiated germ line. The lack of a germ line prevents telomere shortening which can lead to the transfer of somatic mutations into sexual offspring, while sectoriality in trees causes isolation of potentially catastrophic events in one tree part, thus creating a population of more or less independent modules within one axis. The processes of population dynamics, including ageing, can act within the framework of an individual tree as well as in that of the population as a whole, although the processes involved differ and consequently result in different effects.

A potato skin SSH library yields new candidate genes for suberin biosynthesis and periderm formation

Potato (Solanum tuberosum) tubers are underground storage organs covered by the skin or periderm, a suberized layer that protects inner flesh from dehydration and pathogens. Understanding the molecular processes associated with periderm formation is of great importance for a better knowledge of this protective tissue and for improving the storage life of tubers. Here, to isolate new candidate genes for potato periderm, a suppression subtractive hybridization library from potato skin was performed. This library yielded a comprehensive list of 108 candidate genes that were manually sorted in functional categories according to the main cellular and metabolic processes in periderm. As expected, the list contains Suberin and wax genes, including some genes with a demonstrated role in the biosynthesis of these cell wall aliphatic compounds. Moreover, Regulation and Stress and defence genes are highly abundant in the library in general agreement with previous potato skin proteomic studies. The putative function of the genes in periderm is discussed.

Molecular fingerprinting by PCR-denaturing gradient gel electrophoresis reveals differences in the levels of microbial diversity for musty-earthy tainted corks

The microbial community structure of cork with marked musty-earthy aromas was analyzed using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Cork stoppers and discs were used for DNA extraction and were analyzed by using selective primers for bacteria and fungi. Stoppers clearly differed from discs harboring a different fungal community. Moreover, musty-earthy samples of both types were shown to have a specific microbiota. The fungi Penicillium glabrum and Neurospora spp. were present in all samples and were assumed to make only a small contribution to off-odor development. In contrast, Penicillium islandicum and Penicillium variabile were found almost exclusively in 2,4,6-trichloroanisole (TCA) tainted discs. Conversely, Rhodotorula minuta and Rhodotorula sloofiae were most common in cork stoppers, where only small amounts of TCA were detected. Alpha- and gammaproteobacteria were the most commonly found bacteria in either control or tainted cork stoppers. Specific Pseudomonas and Actinobacteria were detected in stoppers with low amounts of TCA and 2-methoxy-3,5-dimethylpyrazine. These results are discussed in terms of biological degradation of taint compounds by specific microorganisms. Reliable and straightforward microbial identification methods based on a molecular approach provided useful data to determine and evaluate the risk of taint formation in cork.

Age-specific, density-dependent and environment-based mortality of a short-lived perennial herb

Density-independent and density-dependent processes affect plant mortality. Although less well understood, age-specific mortality can also play an important role in plant mortality. The goal of this study was to analyse several factors accounting for mortality in the Mediterranean short-lived perennial herb Lobularia maritima. We followed three cohorts of plants (from emergence to death) during 4 years in field conditions. We collected data on plant mortality of the effect of biotic agents (moth larvae and mycoplasma-like organisms, MLOs) and environmental variables. We also estimated density-dependent relationships affecting the fate of seedlings and adults. Results show that cohorts differed in their survival curves and ageing significantly increased mortality risk. Seedling mortality was density-dependent whereas adult mortality was not affected by density. MLO infection led to higher plant mortality whereas moth larvae attack did not affect plant mortality. In general, seedlings and adult plants experienced the highest mortality events in summer. We found, however, weak relationships between weather records and plant mortality. Age and size structures were not correlated. Overall, this study provides a comprehensive review of age-specific, density-dependent and density-independent factors that account for mortality of L. maritima plants throughout their life cycle in field conditions, highlighting the fact that age is an important factor in determining plant population dynamics.

A genomic approach to suberin biosynthesis and cork differentiation

Cork (phellem) is a multilayered dead tissue protecting plant mature stems and roots and plant healing tissues from water loss and injuries. Cork cells are made impervious by the deposition of suberin onto cell walls. Although suberin deposition and cork formation are essential for survival of land plants, molecular studies have rarely been conducted on this tissue. Here, we address this question by combining suppression subtractive hybridization together with cDNA microarrays, using as a model the external bark of the cork tree (Quercus suber), from which bottle cork is obtained. A suppression subtractive hybridization library from cork tree bark was prepared containing 236 independent sequences; 69% showed significant homology to database sequences and they corresponded to 135 unique genes. Out of these genes, 43.5% were classified as the main pathways needed for cork biosynthesis. Furthermore, 19% could be related to regulatory functions. To identify genes more specifically required for suberin biosynthesis, cork expressed sequence tags were printed on a microarray and subsequently used to compare cork (phellem) to a non-suberin-producing tissue such as wood (xylem). Based on the results, a list of candidate genes relevant for cork was obtained. This list includes genes for the synthesis, transport, and polymerization of suberin monomers such as components of the fatty acid elongase complexes, ATP-binding cassette transporters, and acyltransferases, among others. Moreover, a number of regulatory genes induced in cork have been identified, including MYB, No-Apical-Meristem, and WRKY transcription factors with putative functions in meristem identity and cork differentiation.

Acute exposure to UVB has a more profound effect on plant genome stability than chronic exposure

Environmental factors that damage DNA have various lengths of exposure and intensity levels. Although the results of increasing the intensity of a DNA damaging agent is often predictable, it is not clear whether the stage during development when the exposure is received has any influence on the amount of DNA damage. In this paper we analyzed the influence of UVB on the stability of Arabidopsis thaliana and the Nicotiana tabacum genomes. Our experiments showed that the acute exposure to UVB produces a significantly greater increase in homologous recombination frequency (HRF) and recombination rate (RR) compared with that produced by chronic exposure. The increase in HRF showed a positive correlation with UVB dose and a negative correlation with plant age. In other words, as the UVB dose was increased, there was a concomitant increase in HRF. Conversely, older plants had a lower HRF increase as compared to younger plants. Our experiments suggest that exposure to UVB makes the most significant impact on genome stability during the early stages of plant development.

Aging is a deprivation syndrome driven by a germ-soma conflict

Evolution through natural selection can be described as driven by a perpetual conflict of individuals competing for limited resources. Recently, I postulated that the shortage of resources godfathered the evolutionary achievements of the differentiation-apoptosis programming [Rev. Neurosci. 12 (2001) 217]. Unicellular deprivation-induced differentiation into germ cell-like spores can be regarded as the archaic reproduction events which were fueled by the remains of the fratricided cells of the apoptotic fruiting body. Evidence has been accumulated suggesting that conserved through the ages as the evolutionary legacy of the germ-soma conflict, the somatic loss of immortality during the ontogenetic segregation of primordial germ cells recapitulates the archaic fate of the fruiting body. In this heritage, somatic death is a germ cell-triggered event and has been established as evolutionary-fixed default state following asymmetric reproduction in a world of finite resources. Aging, on the other hand, is the stress resistance-dependent phenotype of the somatic resilience that counteracts the germ cell-inflicted death pathway. Thus, aging is a survival response and, in contrast to current beliefs, is antagonistically linked to death that is not imposed by group selection but enforced upon the soma by the selfish genes of the "enemy within". Environmental conditions shape the trade-off solutions as compromise between the conflicting germ-soma interests. Mechanistically, the neuroendocrine system, particularly those components that control energy balance, reproduction and stress responses, orchestrate these events. The reproductive phase is a self-limited process that moulds onset and progress of senescence with germ cell-dependent factors, e.g. gonadal hormones. These degenerate the regulatory pacemakers of the pineal-hypothalamic-pituitary network and its peripheral, e.g. thymic, gonadal and adrenal targets thereby eroding the trophic milieu. The ensuing cellular metabolic stress engenders adaptive adjustments of the glucose-fatty acid cycle, responses that are adequate and thus fitness-boosting under fuel shortage (e.g. during caloric restriction) but become detrimental under fuel abundance. In a Janus-faced capacity, the cellular stress response apparatus expresses both tolerogenic and mutagenic features of the social and asocial deprivation responses [Rev. Neurosci. 12 (2001) 217]. Mediated by the derangement of the energy-Ca(2+)-redox homeostatic triangle, a mosaic of dedifferentiation/apoptosis and mutagenic responses actuates the gradual exhaustion of functional reserves and eventually results in a multitude of aging-related diseases. This scenario reconciles programmed and stochastic features of aging and resolves the major inconsistencies of current theories by linking ultimate and proximate causes of aging. Reproduction, differentiation, apoptosis, stress response and metabolism are merged into a coherent regulatory network that stages aging as a naturally selected, germ cell-triggered and reproductive phase-modulated deprivation response.