Auxin conjugates are thought to play important roles as storage forms for the active plant hormone indole-3-acetic acid (IAA). In its free form, IAA comprises only up to 25% of the total amount of IAA, depending on the tissue and the plant species studied. The major forms of IAA conjugate are low molecular weight ester or amide forms, but there is increasing evidence of the occurrence of peptides and proteins modified by IAA. Since the discovery of genes and enzymes involved in synthesis and hydrolysis of auxin conjugates, much knowledge has been gained on the biochemistry and function of these compounds, but there is still much to discover. For example, recent work has shown that some auxin conjugate hydrolases prefer conjugates with longer-chain auxins such as indole-3-propionic acid and indole-3-butyric acid as substrate. Also, the compartmentation of these reactions in the cell or in tissues has not been resolved in great detail. The function of auxin conjugates has been mainly elucidated by mutant analysis in genes for synthesis or hydrolysis and a possible function for conjugates inferred from these results. In the evolution of land plants auxin conjugates seem to be connected with the development of certain traits such as embryo, shoot, and vasculature. Most likely, the synthesis of auxin conjugates was developed first, since it has been already detected in moss, whereas sequences typical of auxin conjugate hydrolases were found according to database entries first in moss ferns. The implications for the regulation of auxin levels in different species will be discussed.

Auxin conjugates: their role for plant development and in the evolution of land plants

The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has served as a comprehensive repository of bacterial virulence factors (VFs) for >7 years. Bacterial virulence is an exciting and dynamic field, due to the availability of complete sequences of bacterial genomes and increasing sophisticated technologies for manipulating bacteria and bacterial genomes. The intricacy of virulence mechanisms offers a challenge, and there exists a clear need to decipher the ‘language’ used by VFs more effectively. In this article, we present the recent major updates of VFDB in an attempt to summarize some of the most important virulence mechanisms by comparing different compositions and organizations of VFs from various bacterial pathogens, identifying core components and phylogenetic clades and shedding new light on the forces that shape the evolutionary history of bacterial pathogenesis. In addition, the 2012 release of VFDB provides an improved user interface.

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VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short- (6 h) and long- (2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.

/pdf/in-posidonia-oceanica-cadmium-induces-changes-in-dna-3cu7uj83mr.pdf

In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning

The present invention provides a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding an F-box Skp2-like polypeptide, or a DUF584 polypeptide. The present invention also provides plants having modulated expression of a nucleic acid encoding an F-box Skp2-like polypeptide, or a DUF584 polypeptide, which plants have enhanced yield-related traits compared to control plants.

Plants having enhanced yield-related traits and a method for making the same

Auxin is a plant hormone involved in an extraordinarily broad variety of biological mechanisms. These range from basic cellular processes, such as endocytosis, cell polarity, and cell cycle control over localized responses such as cell elongation and differential growth, to macroscopic phenomena such as embryogenesis, tissue patterning, and de novo formation of organs. Even though the history of auxin research reaches back more than a hundred years, we are still far from a comprehensive understanding of how auxin governs such a wide range of responses. Some answers to this question may lie in the auxin molecule itself. Naturally occurring auxin-like substances have been found and they may play roles in specific developmental and cellular processes. The molecular mode of auxin action can be further explored by the utilization of synthetic auxin-like molecules. A second area is the perception of auxin, where we know of three seemingly independent receptors and signalling systems, some better understood than others, but each of them probably involved in distinct physiological processes. Lastly, auxin is actively modified, metabolized, and intracellularly compartmentalized, which can have a great impact on its availability and activity. In this review, we will give an overview of these rather recent and emerging areas of auxin research and try to formulate some of the open questions. Without doubt, the manifold facets of auxin biology will not cease to amaze us for a long time to come.

/pdf/auxin-simply-complicated-9bbyphdyi0.pdf

Auxin: simply complicated

The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity. We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.

/pdf/matgat-an-application-that-generates-similarity-identity-4g3htllozp.pdf

MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.

Anthocyanin pigments aid in reproduction and provide ultraviolet protection to land plants. We have examined the phylogenetic relationships among the five primary enzymes responsible for producing anthocyanin pigment in its three major forms. Dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), Flavonoid 3’glucosyltransferase (F3GT), flavonoid 3’hydroxylase (F3’H), and flavonoid 3’5’ hydroxylase (F3’5’H) are responsible for the final steps in anthocyanin pigment production. We were interested in how conserved the anthocyanin pathway genes may be among land plants, and evolutionarily how far back into the plant lineage anthocyanin production may be traced. The DFR, ANS, F3GT, and F3’H genes date back 450 million years to the first land plants. Mosses, spike mosses, and ferns express these four products, although there is no evidence of sequence orthologues for these genes in algae. Additionally, F3’5’H is not evident in organisms that predated gymnosperms. Our findings support the hypothesis that “blue” anthocyanin pigments did not evolve until 300-350 mya along with the gymnosperms, although the “red” anthocyanin pigments may be as ancient as the mosses (~450 mya).

/pdf/a-phylogenetic-examination-of-the-primary-anthocyanin-7xjgtkmth0.pdf

A phylogenetic examination of the primary anthocyanin production pathway of the Plantae

The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid.We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny. The members of the ILR1-like family analysed were ILL1, ILL2, ILL3, ILL6, ILR1 and IAR3. Present evidence suggests that IAR3 has undergone the least evolution and is most conserved. This conclusion is based on IAR3 having the largest number of total interspecific orthologues, orthologous species and unique orthologues. Although less conserved than IAR3, DNA and protein sequence analyses of ILL1 and ILR1 suggest high conservation. Based on this conservation, IAR3, ILL1 and ILR1 may have had major roles in the physiological evolution of ‘higher’ plants. ILL3 is least conserved, with the fewest orthologous species and orthologues. The monocotyledonous orthologues for most family-members examined have evolved into two separate molecular clades from dicotyledons, indicating active evolutionary change. The monocotyledon clades are: (a) those possessing a putative endoplasmic reticulum localizing signal; and (b) those that are putative cytoplasmic hydrolases. IAR3, ILL1 and ILL6 are all highly orthologous to a gene in the gymnosperm Pinus taeda, indicating an ancient enzymatic activity. No orthologues could be detected in Chlamydomonas, moss and fern databases.

/pdf/a-molecular-phylogenomic-analysis-of-the-ilr1-like-family-of-20cjb7tbn9.pdf

A molecular phylogenomic analysis of the ILR1‐like family of IAA amidohydrolase genes

The phylogenetics of the genus Alphavirus have historically been characterized using partial gene, single gene or partial proteomic data. We have mined cDNA and amino acid sequences from GenBank for all fully sequenced and some partially sequenced alphaviruses and generated phylogenomic analyses of the genus Alphavirus genus, employing capsid encoding structural regions, non-structural coding regions and complete viral genomes. Our studies support the presence of the previously reported recombination event that produced the Western Equine Encephalitis clade, and confirm many of the patterns of geographic radiation and divergence of the multiple species. Our data suggest that the Salmon Pancreatic Disease Virus and Sleeping Disease Virus are sufficiently divergent to form a separate clade from the other alphaviruses. Also, unlike previously reported studies employing limited sequence data for correlation of phylogeny, our results indicate that the Barmah Forest Virus and Middelburg Virus appear to be members of the Semliki Forest clade. Additionally, our analysis indicates that the Southern Elephant Seal Virus is part of the Semliki Forest clade, although still phylogenetically distant from all known members of the genus Alphavirus. Finally, we demonstrate that the whole Rubella viral genome provides an ideal outgroup for phylogenomic studies of the genus Alphavirus.

/pdf/a-phylogenomic-study-of-the-genus-alphavirus-employing-whole-5dgrnj76gr.pdf

A phylogenomic study of the genus Alphavirus employing whole genome comparison.

Zostera marina (eelgrass) can be found in the North Atlantic on the coast of Europe and on the east and west coasts of North America. Over the last 30 years, this once robust species has been reduced to sparse patchy populations due to disease and anthropogenic effects. In order to better understand the consequences of this devastation on the population genetics of the species, we have analyzed the population structure of western Atlantic Z. marina, employing microsatellite DNA polymorphisms. Although high fixation index values suggest moderate genetic differentiation among most of the Z. marina sites, population diversity was low. This lack of diversity was supported by a general dearth of observable heterozygotes in these sites; mean observed heterozygosity values (0.14‐0.46) were lower than the mean expected heterozygosity values (0.57‐0.81). Additionally, the mean FIS (coefficient of local inbreeding) values in these sites were positive, again indicating a surfeit of homozygotes. Allelic richness suggests that Chesapeake Bay has the greatest internal genetic diversity of the sites studied. Inbreeding seems prevalent in these American populations, suggesting possible reproductive fitness problems in the future. There is evidence of demographic bottlenecking and particularly low genetic diversity in Long Island. Northern Maine had the highest effective population size, suggesting a possible use in future restoration projects.

/pdf/population-structure-of-zostera-marina-eelgrass-on-the-3wp83d8ggb.pdf

John V. Smalley

Papers

MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.

A phylogenetic examination of the primary anthocyanin production pathway of the Plantae

A molecular phylogenomic analysis of the ILR1‐like family of IAA amidohydrolase genes

A phylogenomic study of the genus Alphavirus employing whole genome comparison.

Population Structure of Zostera marina (Eelgrass) on the Western Atlantic Coast Is Characterized by Poor Connectivity and Inbreeding