From cyanobacteria to plants: conservation of PII functions during plastid evolution

This article reviews the current state-of-the-art concerning the functions of the signal processing protein PII in cyanobacteria and plants, with a special focus on evolutionary aspects. We start out with a general introduction to PII proteins, their distribution, and their evolution. We also discuss PII-like proteins and domains, in particular, the similarity between ATP-phosphoribosyltransferase (ATP-PRT) and its PII-like domain and the complex between N-acetyl-l-glutamate kinase (NAGK) and its PII activator protein from oxygenic phototrophs. The structural basis of the function of PII as an ATP/ADP/2-oxoglutarate signal processor is described for Synechococcus elongatus PII. In both cyanobacteria and plants, a major target of PII regulation is NAGK, which catalyzes the committed step of arginine biosynthesis. The common principles of NAGK regulation by PII are outlined. Based on the observation that PII proteins from cyanobacteria and plants can functionally replace each other, the hypothesis that PII-dependent NAGK control was under selective pressure during the evolution of plastids of Chloroplastida and Rhodophyta is tested by bioinformatics approaches. It is noteworthy that two lineages of heterokont algae, diatoms and brown algae, also possess NAGK, albeit lacking PII; their NAGK however appears to have descended from an alphaproteobacterium and not from a cyanobacterium as in plants. We end this article by coming to the conclusion that during the evolution of plastids, PII lost its function in coordinating gene expression through the PipX-NtcA network but preserved its role in nitrogen (arginine) storage metabolism, and subsequently took over the fine-tuned regulation of carbon (fatty acid) storage metabolism, which is important in certain developmental stages of plants.     

Ion regulation in invertebrates: molecular and integrative aspects

The subject of ion regulation in invertebrates is discussed, using a variety of invertebrate model species and approaches that range from the whole-organism level to tissue, subcellular, and molecular levels to illustrate the future direction of the field. These organisms inhabit a variety of aquatic, freshwater, and terrestrial environments, showing specific adaptations to each environment. This overview discusses mechanisms of metal detoxification and the presence of Cl-ATPase in marine organisms to avoid excess intracellular Cl(-); Ca(2+) regulation and endocrine aspects of adaptations to transitional (semiterrestrial) environments; adaptations to Ca(2+)-poor freshwater, particularly the reabsorption of Ca(2+) through specific transporters found in the urine; and finally, ionoregulatory mechanisms for life on land, such as Ca(2+) conservation during molting in isopods and the presence of K(+) channels in insect Malpighian tubules. Convergent mechanisms for dealing with similar problems in dissimilar habitats are discussed, taking into consideration that invertebrates will continue to serve as model systems for the evolution of ionoregulation in different habitats.     

Remodeling the model organism: matrix metalloproteinase functions in invertebrates

The matrix metalloproteinase (MMP) family of extracellular proteases is conserved throughout the animal kingdom. Studies of invertebrate MMPs have demonstrated they are involved in tissue remodeling. In Drosophila, MMPs are required for histolysis, tracheal growth, tissue invasion, axon guidance, and dendritic remodeling. Recent work demonstrates that MMPs also participate in Drosophila tumor invasion. In Caenorhabditis elegans an MMP is involved in anchor cell invasion; a Hydra MMP is important for regeneration and maintaining cell identity; and a sea urchin MMP degrades matrix to allow hatching. In worms and in flies, MMPs are regulated by the JNK pathway.     

Essential molecular functions associated with the circular code evolution

A circular code is a set of trinucleotides allowing the reading frames in genes to be retrieved locally, i.e. anywhere in genes and in particular without start codons, and automatically with a window of few nucleotides. In 1996, a common circular code, called X, was identified in large populations of eukaryotic and prokaryotic genes. Hence, it is believed to be an ancestral structural property of genes. A new computational approach based on comparative genomics is developed to identify essential molecular functions associated with circular codes. It is based on a quantitative and sensitive statistical method (FPTF) to identify three permuted trinucleotide sets in the three frames of genes, a flower automaton algorithm to determine if a trinucleotide set is a circular code or not, and an integrated Gene Ontology and Taxonomy (iGOT) database. By carrying out automatic circular code analyses on a huge number of gene populations where each population is associated with a particular molecular function, it identifies 266 gene populations having circular codes close to X. Surprisingly, their molecular functions include 98% of those covered by the essential genes of the DEG database (Database of Essential Genes). Furthermore, three trinucleotides GTG, AAG and GCG, replacing three trinucleotides of the code X and called “evolutionary” trinucleotides, significantly occur in these 266 gene populations. Finally, a new method developed to analyse and quantify the stability of a set of trinucleotides demonstrates that these evolutionary trinucleotides are associated with a significant increase of the stability of the common circular code X. Indeed, its stability increases from the 1502th rank to the 16th rank after the replacement of the three evolutionary trinucleotides among 9920 possible trinucleotide replacement sets.     

Endemism and evolution in Hawaiian marine invertebrates

Endemism in Hawaiian marine invertebrates is strikingly lower than that in Hawaiian terrestrial organisms. Although marine speciation has been widespread, there have been no major radiations or species swarms comparable with those commonly reported for terrestrial animals and plants; the marine fauna of the Hawaiian islands is differentiated from its Indo-west Pacific roots but has not diversified. The marked differences between marine and terrestrial endemism provide broad support for several models in which speciation depends on dispersal, colonization rate, or effective population size. Distinguishing among these models will require detailed information on the genetic structure and phylogenies of marine species both in the Hawaiian archipelago and throughout the Pacific.     

Rate variation during molecular evolution: creationism and the cytochrome c molecular clock

Molecular clocks based upon amino acid sequences in proteins have played a major role in the clarification of evolutionary phylogenies. Creationist criticisms of these methods sometimes rely upon data that might initially seem to be paradoxical. For example, human cytochrome c differs from that of an alligator by 13 amino acids but differs by 14 amino acids from a much more closely related primate, Otolemur garnettii. The apparent anomaly is resolved by taking into consideration the variable substitution rate of cytochrome c, particularly among primates. This paper traces some of the history of extensive research into the topic of rate heterogeneity in cytochrome c including data from cytochrome c pseudogenes.     

Functional and morphological stasis during molecular evolution

The evolutionary distance between two sets of proteins was estimated using the techniques of Miyata and Yasunaga (1980) and Kimura (1980). Human beta 2-microglobulin was compared with the homologous murine molecule, while human and equine alpha-globin were similarly treated. It was found that a large amount of molecular evolution has occurred in beta 2-microglobulin since its divergence from the common ancestor of mice and humans. Kimura's estimate of evolutionary distance, K, is 0.353, while those of Miyata and Yasunaga are KS = 0.708 and KA = 0.171. The respective values for human and equine alpha-globin are 0.152, 0.293, and 0.084. In spite of this molecular evolution, it is shown that murine beta 2-microglobulin can effect the expression of HLA class I antigens on the surface of human-mouse hybrid cells and that the tertiary structures of human and equine deoxyhemoglobin are nearly identical. These observations are discussed in the light of Kimura's theory of neutral allelic drift.     

The evolution of developmental strategy in marine invertebrates

Developmental mode varies widely in most animal phyla. These differences in developmental strategy exert a profound influence on the ecology and evolution of closely related species. The mechanistic alterations in ontogeny that lead to switches in developmental mode are coming under increasing scrutiny. Echinoids are one of the best-understood groups in this regard. Parallel modifications in direct-developing echinoids point to some of the key changes in oogenesis and embryogenesis that produce switches in developmental mode.     

Fibronectin in evolution: presence in invertebrates and isolation from Microciona prolifera

Fibronectin is found in the tissues of a series of vertebrates and invertebrates which suggests its appearance with the simplest multicellular organisms. Fibronectin is specifically localized on the surface and on the substrate in the immediate vicinity of some, but not all, dissociated Microciona prolifera cells, suggesting that the expression of fibronectin in this organism might be dependent on cell type and/or developmental stage. Fibronectin has been partially purified and characterized from intact Microciona prolifera tissue on the basis of its immunological and biochemical properties.     

Seed mucilage evolution: Diverse molecular mechanisms generate versatile ecological functions for particular environments

Plant myxodiasporous species have the ability to release a polysaccharidic mucilage upon imbibition of the seed (myxospermy) or the fruit (myxocarpy). This is a widespread capacity in angiosperms providing multiple ecological functions including higher germination efficiency under environmental stresses. It is unclear whether myxodiaspory has one or multiple evolutionary origins and why it was supposedly lost in several species. Here, we summarize recent advances on three main aspects of myxodiaspory. (a) It represents a combination of highly diverse traits at different levels of observation, ranging from the dual tissular origin of mucilage secretory cells to diverse mucilage polysaccharidic composition and ultrastructural organization. (b) An asymmetrical selection pressure is exerted on myxospermy-related genes that were first identified in Arabidopsis thaliana. The A. thaliana and the flax intra-species mucilage variants show that myxospermy is a fast-evolving trait due to high polymorphism in a few genes directly acting on mucilage establishment. In A. thaliana, these actors are downstream of a master regulatory complex and an original phylogenetic overview provided here illustrates that this complex has sequentially evolved after the common ancestor of seed plants and was fully established in the common ancestor of the rosid clade. (c) Newly identified myxodiaspory ecological functions indicate new perspectives such as soil microorganism control and plant establishment support.     

Kinesin molecular motor Eg5 functions during polypeptide synthesis

The kinesin-related molecular motor Eg5 plays roles in cell division, promoting spindle assembly. We show that during interphase Eg5 is associated with ribosomes and is required for optimal nascent polypeptide synthesis. When Eg5 was inhibited, ribosomes no longer bound to microtubules in vitro, ribosome transit rates slowed, and polysomes accumulated in intact cells, suggesting defects in elongation or termination during polypeptide synthesis. These results demonstrate that the molecular motor Eg5 associates with ribosomes and enhances the efficiency of translation.     

Inositol derivatives: evolution and functions

Current research on inositols mainly focuses on myo-inositol (Ins) derivatives in eukaryotic cells, and in particular on the many roles of Ins phospholipids and polyphosphorylated Ins derivatives. However, inositols and their derivatives are more versatile than this--they have acquired diverse functions over the course of evolution. Given the central involvement of primordial bacteria and archaea in the emergence of eukaryotes, what is the status of inositol derivatives in these groups of organisms, and how might inositol, inositol lipids and inositol phosphates have become ubiquitous constituents of eukaryotes? And how, later, might the multifarious functions of inositol derivatives have emerged during eukaryote diversification?     

无脊椎动物金属硫蛋白(MTs)多样性及其生态服务功能

金属硫蛋白（MTs）是一类低分子量、半胱氨酸含量异常丰富的金属结合多肽,自从20世纪70年代中期发现海洋无脊椎动物MTs以来,MTs已被证明广泛存在于无脊椎动物的各个类群之中。无脊椎动物物种间的金属硫蛋白存在着显著差异,研究无脊椎动物MTs多样性并揭示其生态服务功能,在理论与实践上都至关重要。本文分析了无脊椎动物MTs的多样性：结合金属元素多样性、同形体及其变体的蛋白质遗传多样性和生态服务功能多样性,并讨论了 MTs的三个生态服务功能：MTs对重金属解毒和调节作用、MTs作为环境监测的生物标志物、MTs的环境重金属污染净化功能及其在环境污染治理中的作用。     

Thermal force approach to molecular evolution

Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life.     

Plant ion channels: from molecular structures to physiological functions

Progress in identification of plant ion channels and development of electrophysiological analyses in heterologous expression systems and in planta, in combination with reverse genetic approaches, are providing the possibility of associating molecular entities with physiological functions. Recently, the first attempts to determine in vivo functions using knockout mutants demonstrated the roles of root ion channels. The search for proteins interacting with such channels leads to an even more complex view of the concerted action in protein networks.