Molecular Evolution and Functional Divergence of the Metallothionein Gene Family in Vertebrates

The metallothionein (MT) gene superfamily consists of metal-binding proteins involved in various metal detoxification and storage mechanisms. The evolution of this gene family in vertebrates has mostly been studied in mammals using sparse taxon or gene sampling. Genomic databases and available data on MT protein function and expression allow a better understanding of the evolution and functional divergence of the different MT types. We recovered 77 MT coding sequences from 20 representative vertebrates with annotated complete genomes. We found multiple MT genes, also in reptiles, which were thought to have only one MT type. Phylogenetic and synteny analyses indicate the existence of a eutherian MT1 and MT2, a tetrapod MT3, an amniote MT4, and fish MT. The optimal gene-tree/species-tree reconciliation analyses identified the best root in the fish clade. Functional analyses reveal variation in hydropathic index among protein domains, likely correlated with their distinct flexibility and metal affinity. Analyses of functional divergence identified amino acid sites correlated with functional divergence among MT types. Uncovering the number of genes and sites possibly correlated with functional divergence will help to design cost-effective MT functional and gene expression studies. This will permit further understanding of the distinct roles and specificity of these proteins and to properly target specific MT for different types of functional studies. Therefore, this work presents a critical background on the molecular evolution and functional divergence of vertebrate MTs to carry out further detailed studies on the relationship between heavy metal metabolism and tolerances among vertebrates.     

Fish and molluscan metallothioneins

Metallothioneins (MTs) are noncatalytic peptides involved in storage of essential ions, detoxification of nonessential metals, and scavenging of oxyradicals. They exhibit an unusual primary sequence and unique 3D arrangement. Whereas vertebrate MTs are characterized by the well-known dumbbell shape, with a beta domain that binds three bivalent metal ions and an alpha domain that binds four ions, molluscan MT structure is still poorly understood. For this reason we compared two MTs from aquatic organisms that differ markedly in primary structure: MT 10 from the invertebrate Mytilus galloprovincialis and MT A from Oncorhyncus mykiss. Both proteins were overexpressed in Escherichia coli as glutathione S-transferase fusion proteins, and the MT moiety was recovered after protease cleavage. The MTs were analyzed by gel electrophoresis and tested for their differential reactivity with alkylating and reducing agents. Although they show an identical cadmium content and a similar metal-binding ability, spectropolarimetric analysis disclosed significant differences in the Cd7-MT secondary conformation. These structural differences reflect the thermal stability and metal transport of the two proteins. When metal transfer from Cd7-MT to 4-(2-pyridylazo)resorcinol was measured, the mussel MT was more reactive than the fish protein. This confirms that the differences in the primary sequence of MT 10 give rise to peculiar secondary conformation, which in turn reflects its reactivity and stability. The functional differences between the two MTs are due to specific structural properties and may be related to the different lifestyles of the two organisms.     

中华鳖肝金属硫蛋白的分离、纯化及鉴定（英文）

金属硫蛋白(metallothionein,MT)是一类低分子量、富含半胱氨酸的金属结合蛋白.MT几乎广泛分布于所有生物,包括哺乳动物、两栖动物、鱼、植物、真菌和蓝细菌.不同生物金属硫蛋白理化特性和其氨基酸序列及中心片段的比较研究,对研究MT的结构和生物功能及生物的分子进化提供重要依据.哺乳动物MT研究较多,爬行动物鳖MT的研究尚属空白,本文报道鳖肝的金属硫蛋白.中华鳖 (Pelodiscus sinensis) 分别经皮下注射ZnSO4、CuSO4和CdCl2 溶液诱导后,取乙醇沉淀的肝脏无细胞提取液再经Sephadex G-50、DEAE-SepharoseCL-6B 及SephadexG-25凝胶过滤和离子交换柱层析分离,自鳖肝脏中分别获得Zn-MT、Cu-MT和Cd-MT,未经诱导的鳖肝脏中无MT.质谱和HPLC分析其分子量约为6 300 dalton.根据氨基酸组成分析,鳖肝脏MT含61个氨基酸残基,其中MT的典型氨基酸Cys含量占17%.Lys、Glu和Asp含量较高,而芳香族氨基酸和组氨酸含量极低.从紫外光谱特性分析,Zn-MT、Cu-MT、Cd-MT紫外吸收肩分别在220 nm、270 nm和250 nm.表明确为鳖肝脏MT.从氨基酸残基数和分子量看,鳖肝脏MT与哺乳动物MT类似;而从氨基酸组成和结合金属离子的量看,又与低等生物蚯蚓及酵母菌的MT类似.鳖MT的特性介于哺乳动物MT与低等生物MT之间,体现了鳖这种生物进化的特点.     

中华鳖肝金属硫蛋白的分离、纯化及鉴定

金属硫蛋白metallothionein,MT)是一类低分子量、富含半胱氨酸的金属结合蛋白。MT几乎广泛分布于所有生物,包括哺乳动物、两栖动物、鱼、植物、真菌和蓝细菌,不同生物金属硫蛋白理化特性和其氨基酸序列及中心片段的比较研究,对研究MT的结构和生物功能及生物的分子进化提供重要依据。哺乳动物MT研究较多,爬行动物鳖MT的研究尚属空白,本文报道鳖肝的金属硫蛋白,中华鳖（Pelodiscus sinensis)分别经皮下注射ZnSO4,CuSO4和CdCl2溶液诱导后,取乙醇沉淀的肝脏无细胞提取液再经SephadexG-50、DEAE-SepharoseCL-6B及SephadexG-25凝胶过滤和离子交换柱层析分离,自鳖肝脏中分别获得Zn-MT、Cu-MT和Cd-MT,未经诱导的鳖肝脏中无MT,质谱和HPLC分析其分子量约为6300dalton。根据氨基酸组成分析。鳖肝脏MT含61个氨基酸残基,其中MT的典型氨基酸Cys含量占17%。Lys,Glu和Asp含量较高,而芳香族氨基酸和组氨酸含量极低,从紫外光谱特性分析,Zn-MT、Cu-MT、Cd-MT紫外吸收肩分别在220nm、270nm和250nm。表明确为鳖肝脏MT。从氨基酸残基数和分子量看,鳖肝脏MT与哺乳动物MT类似;而从氨基酸组成和结合金属离子的量看,又与低等生物蚯蚓酵母菌的MT类似。鳖MT的特性介于哺乳动物MT与低等生物MT之间,体现了鳖这种生物进化的特点。     

Erratum

The biochemical features of metallothioneins and their functional role in the cell are described. On this basis, the potential role of MTs as a biomarker of exposure in aquatic organisms, such as fishes and molluscs, is evaluated in the light of recent knowledge about MT gene regulation and inducibility. It appears that in fish MTs should be considered as a kind of stress protein which is particularly responsive to heavy metals. In molluscs, in particular in mussels, MTs seem more specifically involved in responses to heavy metals and they should therefore be considered a biomarker of exposure to heavy metal pollution. Common techniques for MT evaluation are listed and a simple spectrophotometric method recently developed is also reported. Finally, the correct approach to the use of MTs as a biomarker of exposure in biomonitoring programmes for an assessment of the physiological status of aquatic organisms is discussed.     

Metallothionein as a tool in biomonitoring programmes

The biochemical features of metallothioneins and their functional role in the cell are described. On this basis, the potential role of MTs as a biomarker of exposure in aquatic organisms, such as fishes and molluscs, is evaluated in the light of recent knowledge about MT gene regulation and inducibility. It appears that in fish MTs should be considered as a kind of stress protein which is particularly responsive to heavy metals. In molluscs, in particular in mussels, MTs seem more specifically involved in responses to heavy metals and they should therefore be considered a biomarker of exposure to heavy metal pollution. Common techniques for MT evaluation are listed and a simple spectrophotometric method recently developed is also reported. Finally, the correct approach to the use of MTs as a biomarker of exposure in biomonitoring programmes for an assessment of the physiological status of aquatic organisms is discussed.     

水生动物金属硫蛋白分子毒理学研究进展

随着现代工业的迅速发展,重金属污染问题日益严重。重金属离子主要通过水及食物进入生物机体并累积,对机体的生长发育与新陈代谢产生危害。金属硫蛋白（MT）是一种低分子量、富含半胱氨酸的蛋白质,广泛存在于大多数生物体内,在必需金属元素稳态调节、非必需金属元素解毒以及抗氧化等过程中具有重要作用,因此,MT可作为检测水生生态系统中重金属污染的潜在生物标记,其分子毒理学已成为研究热点。综述了MT的结构、功能、分类与分布,以及鱼类、甲壳类和软体动物的MT分子毒理学研究概况。     

To Investigate Protein Evolution by Detecting Suppressed Epitope Structures

Material remains of ancestor nucleotides and proteins are largely unavailable, thus sequence comparison among homologous genes in present-day organisms forms the core of current knowledge of molecular evolution. Variation in protein three-dimensional structure is a basis for functional diversity. To study the evolution of three-dimensional structures in related proteins would significantly improve our understanding of protein evolution and function. A protein may contain ancestor conformations that have been allosterically suppressed by evolutionarily additive structures. Using monoclonal antibody probes to detect such conformation in proteins after removing the suppressor structure, our study demonstrates three-dimensional structure evidence for the evolutionary relationship between troponin I and troponin T, two subunits of the troponin complex in the Ca²⁺-regulatory system of striated muscle, and among their muscle type-specific isoforms. The experimental data show the feasibility of detecting evolutionarily suppressed history-telling structural states in proteins by removing conformational modulator segments added during evolution. In addition to identifying structural modifications that were critical to the emergence of diverged proteins, investigating this novel mode of evolution will help us to understand the origin and functional potential of protein structures.     

Challenging the model for induction of metallothionein gene expression

Metallothioneins (MTs) are low-molecular-weight, cysteine-rich metal-binding proteins found in a wide variety of organisms including bacteria, fungi and all eukaryotic plant and animal species. MTs bind essential and non-essential heavy metals. In mammalian cells MT genes are highly inducible by many heavy metals including Zn, Cd, Hg, and Cu. Aquatic systems are contaminated by different pollutants, including metals, as a result of man's activities. Bivalve molluscs are known to accumulate high concentrations of heavy metals in their tissue and are widely used as bioindicators for pollution in marine and freshwater environments, with MTs frequently used as a valuable marker of metal contamination. We here describe the MT isoform gene expression patterns of marine and freshwater molluscs and fish species after Cd or Zn contamination. Contamination was carried out at a river site polluted by a zinc ore extraction plant or in the laboratory at low, environmentally relevant metal concentrations. A comparison for each species based on the accumulated MT protein levels often shows discrepancies between gene expression and protein level. In addition, several differences observed in the pattern of MT gene expression between mollusc and mammalian species enable us to discuss and challenge a model for the induction of MT gene expression.     

Comparative study of ammonium transporters in different organisms by study of a large number of structural protein features via data mining algorithms

Ammonium is an excellent nitrogen source, and ammonium transfer is a fundamental process in most organisms. Membrane transport of ammonium is the key component of nitrogen metabolism mediated by Ammonium Transporter/Methylamine Permease/Rhesus (AMT/MEP/Rh) protein family. Ammonium transporters play different physiological roles in various organisms. Here, we looked at the protein characteristics of ammonium transporters in different organisms to create a link between protein characteristics and the organism. In order to increase the accuracy and precision of the employed models, for the first time, an attempt was made to cover all structural aspects of ammonium transporters in animals, bacteria, fungi, plants, and human by extracting and calculating 874 protein attributes of primary, secondary, and tertiary structures for each ammonium transporter. Then, various weighting and modeling algorithms were applied to determine how structural protein features change between organisms. Considering a large number of protein attributes made it possible to detect key protein characteristics in the structure of ammonium transporters. The results, for the first time, indicated that His-based features including count/frequency of His and frequency/count of Ile-His were the most significant features generating different types of ammonium transporters within organisms. Within different tested models, the C5.0 model was the most efficient and precise model for discrimination of organism type, based on ammonium transporter sequence, with the precision of 94.85%. The determination of protein characteristics of ammonium transporters in different organisms provides a new vista for understanding the evolution of transporters based on the modulation of protein characteristics and facilitates engineering of new transporters. In our point of view, dissecting a large number of structural protein characteristics through data mining algorithms provides a novel functional strategy for studying evolution and phylogeny. This research will serve as a basis for future studies on engineering novel ammonium transporters.     

Induction, regulation, degradation, and biological significance of mammalian metallothioneins

MTs are small cysteine-rich metal-binding proteins found in many species and, although there are differences between them, it is of note that they have a great deal of sequence and structural homology. Mammalian MTs are 61 or 62 amino acid polypeptides containing 20 conserved cysteine residues that underpin the binding of metals. The existence of MT across species is indicative of its biological demand, while the conservation of cysteines indicates that these are undoubtedly central to the function of this protein. Four MT isoforms have been found so far, MT-1, MT-2, MT-3, and MT-4, but these also have subtypes with 17 MT genes identified in man, of which 10 are known to be functional. Different cells express different MT isoforms with varying levels of expression perhaps as a result of the different function of each isoform. Even different metals induce and bind to MTs to different extents. Over 40 years of research into MT have yielded much information on this protein, but have failed to assign to it a definitive biological role. The fact that multiple MT isoforms exist, and the great variety of substances and agents that act as inducers, further complicates the search for the biological role of MTs. This article reviews the current knowledge on the biochemistry, induction, regulation, and degradation of this protein in mammals, with a particular emphasis on human MTs. It also considers the possible biological roles of this protein, which include participation in cell proliferation and apoptosis, homeostasis of essential metals, cellular free radical scavenging, and metal detoxification.     

Induction,Regulation, Degradation,and Biological Significance of Mammalian Metallothioneins

MTs are small cysteine-rich metal-binding proteins found in many species and, although there are differences between them, it is of note that they have a great deal of sequence and structural homology. Mammalian MTs are 61 or 62 amino acid polypep-tides containing 20 conserved cysteine residues that underpin the binding of metals. The existence of MT across species is indicative of its biological demand, while the conservation of cysteines indicates that these are undoubtedly central to the function of this protein. Four MT isoforms have been found so far, MT-1, MT-2, MT-3, and MT-4, but these also have subtypes with 17 MT genes identified in man, of which 10 are known to be functional. Different cells express different MT isoforms with varying levels of expression perhaps as a result of the different function of each isoform. Even different metals induce and bind to MTs to different extents. Over 40 years of research into MT have yielded much information on this protein, but have failed to assign to it a definitive biological role. The fact that multiple MT isoforms exist, and the great variety of substances and agents that act as inducers, further complicates the search for the biological role of MTs. This article reviews the current knowledge on the biochemistry, induction, regulation, and degradation of this protein in mammals, with a particular emphasis on human MTs. It also considers the possible biological roles of this protein, which include participation in cell proliferation and apoptosis, homeostasis of essential metals, cellular free radical scavenging, and metal detoxification.     

Spectroscopic characterization of a fruit-specific metallothionein: M. acuminata MT3

Metallothioneins (MTs) are ubiquitous low molecular mass, cysteine-rich proteins with the ability to bind d¹⁰ metal ions in the form of metal-thiolate clusters. In contrast to the vertebrate forms, knowledge about the properties of members of the plant metallothionein family is still scarce. The amino acid sequences of plant MTs are distinctively different to the sequences of other MT species. The protein under investigation, Musa acuminata (banana) MT3, belongs to the plant MT fruit-specific p3 subfamily. With a total of 10 cysteine residues, MT3 features a cysteine content and percentage that is more comparable to fungal and prokaryotic MTs than to the well characterized mammalian iso-forms. The gene sequence encoding MT3 was cloned into a suitable vector and the protein was recombinantly overexpressed in Escherichia coli. MT3 is able to coordinate a maximum of four divalent d¹⁰ metal ions under the formation of metal-thiolate clusters. The hitherto unknown spectroscopic behavior of MT3 in combination with the metal ions Zn²⁺, Cd²⁺, Pb²⁺, and Hg²⁺ will be presented and gives rise to the existence of a weaker metal ion coordination site. The pH stability of the investigated zinc and cadmium clusters is comparable to the values found for other plant metallothioneins though significantly lower than for the mammalian iso-forms. Possible metal-thiolate cluster structures will additionally be discussed.     

Metallothionein: a multifunctional protein from toxicity to cancer

The metallothionein (MT) family is a class of low molecular weight, intracellular and cysteine-rich proteins presenting high affinity for metal ions. Although the members of this family were discovered nearly 40 years ago, their functional significance remains obscure. Four major MT isoforms, MT-1, MT-2, MT-3 and MT-4, have been identified in mammals. MTs are involved in many pathophysiological processes such as metal ion homeostasis and detoxification, protection against oxidative damage, cell proliferation and apoptosis, chemoresistance and radiotherapy resistance. MT isoforms have been shown to be involved in several aspects of the carcinogenic process, cancer development and progression. MT expression has been implicated as a transient response to any form of stress or injury providing cytoprotective action. Although MT participates in the carcinogenic process, its use as a potential marker of tumor differentiation or cell proliferation, or as a predictor of poor prognosis remains unclear. In the present review the involvement of MT in defense mechanisms to toxicity and in carcinogenicity is discussed.     

Evo-devo of non-bilaterian animals

The non-bilaterian animals comprise organisms in the phyla Porifera, Cnidaria, Ctenophora and Placozoa. These early-diverging phyla are pivotal to understanding the evolution of bilaterian animals. After the exponential increase in research in evolutionary development (evo-devo) in the last two decades, these organisms are again in the spotlight of evolutionary biology. In this work, I briefly review some aspects of the developmental biology of nonbilaterians that contribute to understanding the evolution of development and of the metazoans. The evolution of the developmental genetic toolkit, embryonic polarization, the origin of gastrulation and mesodermal cells, and the origin of neural cells are discussed. The possibility that germline and stem cell lineages have the same origin is also examined. Although a considerable number of non-bilaterian species are already being investigated, the use of species belonging to different branches of non-bilaterian lineages and functional experimentation with gene manipulation in the majority of the non-bilaterian lineages will be necessary for further progress in this field.     

Local adaptation to biocontrol agents: A multi-objective data-driven optimization model for the evolution of resistance

Spatial and temporal variability in the application of biological control agents such as parasites or pathogenic bacteria can cause the evolution of resistance in pest organisms. Because biocontrol will be more effective if organisms are not resistant, it is desirable to examine the evolution of resistance under different application strategies.We present a computational method that integrates a genetic algorithm with experimental data for predicting when local populations are likely to evolve resistance to biocontrol pathogens. The model incorporates parameters that can be varied as part of pest control measures such as the distribution and severity of the biocontrol agent (e.g., pathogenic fungi). The model predicts the evolution of pathogen defense as well as indirect selection on several aspects of the organism's genetic system. Our results show that both variability of selection within populations as well as mean differences among populations are important in the evolution of defenses against biocontrol pathogens. The mean defense is changed through the pest organism's genotype and the variance is affected by components of the genetic system, namely, the resiliency, recombination rate and number of genes.The data-driven model incorporates experimental data on pathogen susceptibility and the cost of defense. The results suggest that spatial variability rather than uniform application of biological control will limit the evolution of resistance in pest organisms.     

The evolution of optimal emergence times: bet hedging and the quest for an ideal free temporal distribution of individuals

Proper timing of activities is one of the principal challenges faced by most organisms. Organisms need to account for various aspects in decision making like avoiding inordinate risks, synchronizing with resource availability, or finding mates. We provide analytical and simulation models to investigate the influence of life expectancy, resource competition and unpredictable environmental conditions (environmental uncertainty) on the evolutionarily stable distribution of emergence times in organisms depending on seasonally available resources. We focus on the partitioning of total phenotypic variance in emergence times into 1) genetic variance in mean emergence times between lineages and 2) environmental trait variance that determines the intra‐lineage variance in the timing of emergence. Both, life expectancy of organisms and intensity of competition severely influence the evolutionary response to environmental uncertainty. Our main findings can be summarized as follows: 1) in general diversifying bet hedging (environmental trait variance) is the adequate mechanism to reduce the risk arising from environmental uncertainty while conservative bet hedging, i.e. delaying emergence into ‘safe’ phases of the season is restricted to short lived organisms and to situations with vanishing competition. 2) Environmental trait variance increases with increasing environmental uncertainty whereas 3) significant genetic variance evolves only under severe resource competition; it is driven by selection for an ideal free distribution of emergence times. 4) The level of genetic variance evolving declines with increasing life expectancy of organisms. 5) With sufficiently short life expectancy evolutionary branching and coexistence of distinctly different emergence strategies occurs; the number of co‐occurring strategies is determined by the level of environmental uncertainty. Our model provides cues for understanding how different ecological factors contribute and interact to shape the evolution of emergence strategies.