Molecular biology of enzyme adaptations in higher eukaryotes

Multicellular eukaryotes have evolved complex homeostatic mechanisms that buffer the majority of their cells from direct interaction with the external environment. Thus, in these organisms long-term adaptations are generally achieved by modulating the developmental profile and tissue specificity of gene expression. Nevertheless, a subset of eukaryotic genes are still involved in direct responses to environmental fluctuations. It is the adaptative responses in the expression of these genes that buffers many other genes from direct environmental effects. Both microevolutionary and macroevolutionary patterns of change in the structure and regulation of such genes are illustrated by the sequences encoding alpha-amylases. The molecular biology and evolution of alpha-amylases in Drosophila and other higher eukaryotes are presented. The amylase system illustrates the effects of both long-term and short-term natural selection, acting on both the structural and regulatory components of a gene--enzyme system. This system offers an opportunity for linking evolutionary genetics to molecular biology, and it allows us to explore the relationship between short-term microevolutionary changes and long-term adaptations.     

Nitric oxide and nitrosative stress tolerance in yeast

The opportunistic human fungal pathogen Candida albicans encounters diverse environmental stresses when it is in contact with its host. When colonizing and invading human tissues, C. albicans is exposed to ROS (reactive oxygen species) and RNIs (reactive nitrogen intermediates). ROS and RNIs are generated in the first line of host defence by phagocytic cells such as macrophages and neutrophils. In order to escape these host-induced oxidative and nitrosative stresses, C. albicans has developed various detoxification mechanisms. One such mechanism is the detoxification of NO (nitric oxide) to nitrate by the flavohaemoglobin enzyme CaYhb1. Members of the haemoglobin superfamily are highly conserved and are found in archaea, eukaryotes and bacteria. Flavohaemoglobins have a dioxygenase activity [NOD (NO dioxygenase domain)] and contain three domains: a globin domain, an FAD-binding domain and an NAD(P)-binding domain. In the present paper, we examine the nitrosative stress response in three fungal models: the pathogenic yeast C. albicans, the benign budding yeast Saccharomyces cerevisiae and the benign fission yeast Schizosaccharomyces pombe. We compare their enzymatic and non-enzymatic NO and RNI detoxification mechanisms and summarize fungal responses to nitrosative stress.     

Cytokinesis in eukaryotes: a mechanistic comparison

Cytokinesis is a crucial but poorly understood process of cell proliferation. Recently, molecular genetic analyses of fungal cytokinesis have led to an appreciation of contractile mechanisms in simple eukaryotes, and studies in animal and plant cells have led to new insights into the role of microtubules in the cleavage process. These findings suggest that fundamental mechanisms of cytokinesis may be highly conserved among eukaryotic organisms.     

Extremotolerance in fungi: evolution on the edge

Our planet offers many opportunities for life on the edge: high and low temperatures, high salt concentrations, acidic and basic conditions and toxic environments, to name but a few extremes. Recent studies have revealed the diversity of fungi that can occur in stressful environments that are hostile to most eukaryotes. We review these studies here, with the additional purpose of proposing some mechanisms that would allow for the evolutionary adaptation of eukaryotic microbial life under extreme conditions. We focus, in particular, on life in ice and life at high salt concentrations, as there is a surprising similarity between the fungal populations in these two kinds of environments, both of which are characterized by low water activity. We propose steps of evolution of generalist species towards the development of specialists in extreme habitats. We argue that traits present in some fungal groups, such as asexuality, synthesis of melanin-like pigments and a flexible morphology, are preadaptations that facilitate persistence and eventual adaptation to conditions on the ecological edge, as well as biotope switches. These processes are important for understanding the evolution of extremophiles; moreover, they have implications for the emergence of novel fungal pathogens.     

Cellular and mitochondrial iron homeostasis in vertebrates

Iron plays an essential role in cellular metabolism and biological processes. However, due to its intrinsic redox activity, free iron is a potentially toxic molecule in cellular biochemistry. Thus, organisms have developed sophisticated ways to import, sequester, and utilize iron. The transferrin cycle is a well-studied iron uptake pathway that is important for most vertebrate cells. Circulating iron can also be imported into cells by mechanisms that are independent of transferrin. Once imported into erythroid cells, iron is predominantly consumed by the mitochondria for the biosynthesis of heme and iron sulfur clusters. This review focuses on canonical transferrin-mediated and the newly discovered, non-transferrin mediated iron uptake pathways, as well as, mitochondrial iron homeostasis in higher eukaryotes. This article is part of a Special Issue entitled: Cell Biology of Metals.     

真菌有性生殖调控与进化

以真菌为对象的有性生殖机制研究揭示了普遍存在于真核生物中的生物学现象及规律,包括染色体倍性变化、减数分裂形成配子、交配对象识别及细胞一细胞融合形成合子等．真菌的有性生殖由交配型位点控制,除了类似其他真核生物两性生殖的异宗配合外,还包括同宗配合和次级同宗配合,部分物种的单倍体还具有交配型互换的能力．互补交配型的单倍体通过荷尔蒙及其受体进行相互识别,再经过G蛋白偶联受体介导的信号途径调控有性生殖过程及子实体发育,这一过程受多种胞内调控因子及外界环境条件的影响．不同真菌类群生殖方式的演化与物种进化仍缺少统一的规律．进一步研究揭示,真菌有性生殖的调控机制及环境诱导因子,不仅具有重要的理论意义,也有利于促进不同经济真菌子实体的人工培养及高效利用．     

The biological occurrence and trafficking of cobalt

Cobalt is an essential trace element in both prokaryotes and eukaryotes. Nevertheless, it occurs less frequently in metalloproteins than other transition metals. This low occurrence appears to be due to the metal's low abundance in nature as well as its competition with iron, whose biologically critical functions include respiration and photosynthesis. In this review, we discuss the biological role of cobalt, the major effects of cobalt on iron utilization, as well as several mechanisms that cells have developed to circumvent the toxicity of cobalt while still exploiting its chemistry.     

Prokaryotic Sex: Eukaryote-like Qualities of Recombination in an Archaean Lineage

Genetic exchange within one Archaean lineage is a bit like sex in eukaryotes?-?cells fuse and huge segments of DNA are recombined?-?with consequences for the spread of adaptations across species.     

Metal Acquisition and Homeostasis in Fungi

Transition metals, particularly iron, zinc and copper, have multiple biological roles and are essential elements in biological processes. Among other micronutrients, these metals are frequently available to cells in only limited amounts, thus organisms have evolved highly regulated mechanisms to cope and to compete with their scarcity. The homeostasis of such metals within the animal hosts requires the integration of multiple signals producing depleted environments that restrict the growth of microorganisms, acting as a barrier to infection. As the hosts sequester the necessary transition metals from invading pathogens, some, as is the case of fungi, have evolved elaborate mechanisms to allow their survival and development to establish infection. Metalloregulatory factors allow fungal cells to sense and to adapt to the scarce metal availability in the environment, such as in host tissues. Here we review recent advances in the identification and function of molecules that drive the acquisition and homeostasis of iron, copper and zinc in pathogenic fungi.     

Off the hook--how bacteria survive protozoan grazing

Bacterial growth and survival in numerous environments are constrained by the action of bacteria-consuming protozoa. Recent findings suggest that bacterial adaptations against protozoan predation might have a significant role in bacterial persistence and diversification. We argue that selective predation has given rise to diverse routes of bacterial defense, including adaptive mechanisms in bacterial biofilms, and has promoted major transitions in bacterial evolution, such as multicellularity and pathogenesis. We propose that studying predation-driven adaptations will provide an exciting frontier for microbial ecology and evolution at the interface of prokaryotes and eukaryotes.     

Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species

Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.     

病原真菌中潜在的铁死亡通路：功能与研究展望

铁死亡是一种铁离子参与、使细胞内脂质过氧化物积累到致死水平的新型程序性细胞死亡形式。目前,铁死亡的作用与机制在动物细胞已广泛、深入研究,而真菌铁死亡研究才刚刚起步。本综述旨在探讨铁离子稳态调控因子、膜脂抗氧化系统及脂质过氧化酶促系统这3种已知的铁死亡调控途径,列举它们在真菌中的同源蛋白的生物学功能。我们推测,病原真菌细胞铁死亡也许广泛参与其生长发育和致病性方面的调控,铁死亡调控通路有可能成为真菌病害防控的新的潜在靶标。     

Ecology and molecular adaptations of the halophilic black yeast Hortaea werneckii

Molecular studies on halophilic adaptations have focused on prokaryotic microorganisms due to a lack of known appropriate eukaryotic halophilic microorganisms. However, the black yeast Hortaea werneckii has been identified as the dominant fungal species in hypersaline waters on three continents. It represents a new model organism for studying the mechanisms of salt tolerance in eukaryotes. Ultrastructural studies of the H. werneckii cell wall have shown that it synthesizes dihydroxynaphthalene (DHN) melanin under both saline and non-saline growth conditions. However, melanin granules in the cell walls are organized in a salt-dependent way, implying the potential osmoprotectant role of melanin. At the level of membrane structure, H. werneckii maintains a sterol-to-phospholipid ratio significantly lower than the salt-sensitive Saccharomyces cerevisiae. Accordingly, membranes of H. werneckii are more fluid over a wide range of NaCl concentrations, indicating high intrinsic salt stress tolerance. Even H. werneckii grown in high NaCl concentrations maintains very low intracellular amounts of potassium and sodium, demonstrating the sodium-excluder character of this organism. The salt-dependent expressions of two HwENA genes suggest roles for them in the adaptation to changing salt concentrations. The high similarity of these ENA ATPases to other fungal ENA ATPases involved in Na⁺/K⁺ transport indicates their potential importance in H. werneckii ion homeostasis. Glycerol is the main compatible solute which accumulates in the cytoplasm of H. werneckii at high salinity, although it seems that mycosporines may also act as supplementary compatible solutes. Salt dependent increase in glycerol synthesis is supported by the identification of two copies of a gene putatively coding for glycerol-3-phosphate-dehydrogenase. Expression of only one of these genes is salt dependent.     

Control of filamentous fungal cell shape by septins and formins

Studies in various model systems have identified two protein families that are crucial for shaping cell morphology: the septins and the formins. Both families are conserved in most eukaryotes, but the functions and regulation of individual homologues can vary depending on their precise cellular context. The rich array of cell geometries found in different filamentous fungal species provides a powerful experimental canvas for studying the evolution and regulation of septins and formins. Here, I assimilate what is known about the function of these protein families in filamentous fungi and propose that further studies in these organisms could answer some open mechanistic questions that pertain in general to eukaryotic cells.     

Iron and siderophores in fungal–host interactions

Most fungi and bacteria express specific mechanisms for the acquisition of iron from the hosts they infect for their own survival. This is primarily because iron plays a key catalytic role in various vital cellular reactions in conjunction with the fact that iron is not freely available in these environments due to host sequestration. High-affinity iron uptake systems, such as siderophore-mediated iron uptake and reductive iron assimilation, enable fungi to acquire limited iron from animal or plant hosts. Regulating iron uptake is crucial to maintain iron homeostasis, a state necessary to avoid iron-induced toxicity from iron abundance, while simultaneously supplying iron required for biochemical demand. Siderophores play diverse roles in fungal–host interactions, many of which have been principally delineated from gene deletions in non-ribosomal peptide synthetases, enzymes required for siderophore biosynthesis. These analyses have demonstrated that siderophores are required for virulence, resistance to oxidative stress, asexual/sexual development, iron storage, and protection against iron-induced toxicity in some fungal organisms. In this review, the strategies fungi employ to obtain iron, siderophore biosynthesis, and the regulatory mechanisms governing iron homeostasis will be discussed with an emphasis on siderophore function and relevance for fungal organisms in their interactions with their hosts.