Stem-cell niches: nursery rhymes across kingdoms

Despite the large evolutionary distance between the plant and animal kingdoms, stem cells in both reside in specialized cellular contexts called stem-cell niches. Although stem-cell-specification factors have been recruited from plant-specific gene families, maintenance factors that repress stem-cell differentiation are conserved between plants and animals. Recent evidence indicates that stem cells in multicellular organisms can be specified by kingdom-specific patterning mechanisms that connect to a related core of epigenetic stem-cell factors.     

Evolution goes GAGA: GAGA binding proteins across kingdoms

Chromatin-associated proteins (CAP) play a crucial role in the regulation of gene expression and development in higher organisms. They are involved in the control of chromatin structure and dynamics. CAP have been extensively studied over the past years and are classified into two major groups: enzymes that modify histone stability and organization by post-translational modification of histone N-Terminal tails; and proteins that use ATP hydrolysis to modify chromatin structure. All of these proteins show a relatively high degree of sequence conservation across the animal and plant kingdoms. The essential Drosophila melanogaster GAGA factor (dGAF) interacts with these two types of CAP to regulate homeobox genes and thus contributes to a wide range of developmental events. Surprisingly, however, it is not conserved in plants. In this review, following an overview of fly GAF functions, we discuss the role of plant BBR/BPC proteins. These appear to functionally converge with dGAF despite a completely divergent amino acid sequence. Some suggestions are given for further investigation into the function of BPC proteins in plants.     

Septin localization across kingdoms: three themes with variations

Septins are GTPases that form filaments in fungi and animals. In addition to their original role in cell division, septins have been shown to have roles in coordinating nuclear division, membrane trafficking and organizing the cytoskeleton. Many recent studies have examined subcellular localization of septins in a wide range of fungi and animals. Septin localization shows three patterns, which generally correspond to function across kingdoms. Septins that localize to projections shape and compartmentalize emerging growth. Septins that localize to partitions compartmentalize pre-existing cellular material. Septins that localize to the whole cell are involved in membrane trafficking and organizing the cytoskeleton and are most often in animals. The difference in localization pattern frequency between kingdoms will probably disappear as more septins are examined in diverse organisms and tissues.     

At the poles across kingdoms: phosphoinositides and polar tip growth

Phosphoinositides (PIs) are minor, but essential phospholipid constituents of eukaryotic membranes, and are involved in the regulation of various physiological processes. Recent genetic and cell biological advances indicate that PIs play important roles in the control of polar tip growth in plant cells. In root hairs and pollen tubes, PIs control directional membrane trafficking required for the delivery of cell wall material and membrane area to the growing tip. So far, the exact mechanisms by which PIs control polarity and tip growth are unresolved. However, data gained from the analysis of plant, fungal and animal systems implicate PIs in the control of cytoskeletal dynamics, ion channel activity as well as vesicle trafficking. The present review aims at giving an overview of PI roles in eukaryotic cells with a special focus on functions pertaining to the control of cell polarity. Comparative screening of plant and fungal genomes suggests diversification of the PI system with increasing organismic complexity. The evolutionary conservation of the PI system among eukaryotic cells suggests a role for PIs in tip growing cells in models where PIs so far have not been a focus of attention, such as fungal hyphae.     

Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms

Filamentous fungi and oomycetes are eukaryotic microorganisms that grow by producing networks of thread-like hyphae, which secrete enzymes to break down complex nutrients, such as wood and plant material, and recover the resulting simple sugars and amino acids by osmotrophy. These organisms are extremely similar in both appearance and lifestyle and include some of the most economically important plant pathogens . However, the morphological similarity of fungi and oomycetes is misleading because they represent some of the most distantly related eukaryote evolutionary groupings, and their shared osmotrophic growth habit is interpreted as being the result of convergent evolution . The fungi branch with the animals, whereas the oomycetes branch with photosynthetic algae as part of the Chromalveolata . In this report, we provide strong phylogenetic evidence that multiple horizontal gene transfers (HGT) have occurred from filamentous ascomycete fungi to the distantly related oomycetes. We also present evidence that a subset of the associated gene families was initially the product of prokaryote-to-fungi HGT. The predicted functions of the gene products associated with fungi-to-oomycete HGT suggest that this process has played a significant role in the evolution of the osmotrophic, filamentous lifestyle on two separate branches of the eukaryote tree.     

Analysis of septins across kingdoms reveals orthology and new motifs

Background  

Septins are cytoskeletal GTPase proteins first discovered in the fungus Saccharomyces cerevisiae where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison.     

Microtubule drugs: action,selectivity, and resistance across the kingdoms of life

Microtubule drugs such as paclitaxel, colchicine, vinblastine, trifluralin, or oryzalin form a chemically diverse group that has been reinforced by a large number of novel compounds over time. They all share the ability to change microtubule properties. The profound effects of disrupted microtubule systems on cell physiology can be used in research as well as anticancer treatment and agricultural weed control. The activity of microtubule drugs generally depends on their binding to α- and β-tubulin subunits. The microtubule drugs are often effective only in certain taxonomic groups, while other organisms remain resistant. Available information on the molecular basis of this selectivity is summarized. In addition to reviewing published data, we performed sequence data mining, searching for kingdom-specific signatures in plant, animal, fungal, and protozoan tubulin sequences. Our findings clearly correlate with known microtubule drug resistance determinants and add more amino acid positions with a putative effect on drug-tubulin interaction. The issue of microtubule network properties in plant cells producing microtubule drugs is also addressed.     

A general tendency for conservation of protein length across eukaryotic kingdoms

Protein elongation can occur in many ways, such as domain duplication or insertion and as recruitment of a transposable element fragment into the coding region, and it is believed to be a general tendency in protein evolution. Indeed, a previous study showed that yeast proteins are, on average, longer than their orthologs in bacteria, and in this study, we found that proteins in yeast, nematode, Drosophila, human, and Arabidopsis are, on average, longer than their orthologs in Escherichia coli. Surprisingly, however, we found conservation of protein sequence length across eukaryotic kingdoms. We collected 1,252 orthologous proteins from yeast, nematode, Drosophila, human, and Arabidopsis and found that the total length of these proteins is very similar among the five species and that there is no general tendency for a protein to increase or decrease in length. Furthermore, although paralogous proteins tend to undergo more sequence-length changes, there is also no general tendency for length increase. However, proteins that are commonly shared by Drosophila and human but not by yeast are, on average, substantially longer than proteins that are shared by yeast, Drosophila, and human. This is a puzzle that begs for an answer.     

Simulated glacial and interglacial vegetation across Africa: implications for species phylogenies and trans-African migration of plants and animals

The paleoenvironmental context of plant and animal species evolution (including glacial migrations and population separations) is based on a very patchy and incomplete paleo‐phytogeographic record. It was our objective, therefore, to provide an additional source for paleovegetation comparison by presenting simulations from a state‐of‐the‐art fully coupled earth system model (HadCM3LC). We simulated potential paleovegetation distributions following pre‐Industrial and last glacial maximum (LGM) climate forcing for the continent of Africa. Our LGM simulations indicate that tropical broadleaf forest was not severely displaced by expanding grasslands within central Africa, although the outer extent of closed forest decreases, particularly in the north. Our simulations indicate that the structure of glacial forests may have been much different from today, in that LGM simulations indicate that forests were likely characterized by lower leaf area indexes, lower tree heights and lower vegetation carbon content. On the other hand, warmer interglacial climate (like our pre‐Industrial climate scenario) results in simulated expansion of tropical forest from coast to coast across central Africa that we postulate could have acted as a barrier to plant and animal species migrations. We suggest that our modeling experiments have implications for the interpretation of phylogenetic data, including that of our own species, Homo sapiens sapiens.     

Sexual selection in plants and animals

Belated recognition of the evolutionary import of reproductive success through male function in plants has led to the application of sexual selection theory to these organisms. Recent work has shown that there are many parallels, related to sexual selection, in the reproductive processes of animals and of plants, although the proximate mechanisms and evolutionary constraints sometimes differ.     

Allometric scaling in animals and plants

In this paper we give a derivation for the allometric scaling relation between the metabolic rate and the mass of animals and plants. We show that the characteristic scaling exponent of 3/4 occurring in this relation is a result of the distribution of sources and sinks within the living organism. We further introduce a principle of least mass and discuss the kind of flows that arise from it.