Structure,Function, and Evolution of Bacterial ATP-Binding Cassette Systems

Summary: ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.     

Germin and Germin-like Proteins: Evolution,Structure, and Function

Germin and germin-like proteins (GLPs) are encoded by a family of genes found in all plants. They are part of the cupin superfamily of biochemically diverse proteins, a superfamily that has a conserved tertiary structure, though with limited similarity in primary sequence. The subgroups of GLPs have different enzyme functions that include the two hydrogen peroxide–generating enzymes, oxalate oxidase (OxO) and superoxide dismutase. This review summarizes the sequence and structural details of GLPs and also discusses their evolutionary progression, particularly their amplification in gene number during the evolution of the land plants. In terms of function, the GLPs are known to be differentially expressed during specific periods of plant growth and development, a pattern of evolutionary subfunctionalization. They are also implicated in the response of plants to biotic (viruses, bacteria, mycorrhizae, fungi, insects, nematodes, and parasitic plants) and abiotic (salt, heat/cold, drought, nutrient, and metal) stress. Most detailed data come from studies of fungal pathogenesis in cereals. This involvement with the protection of plants from environmental stress of various types has led to numerous plant breeding studies that have found links between GLPs and QTLs for disease and stress resistance. In addition the OxO enzyme has considerable commercial significance, based principally on its use in the medical diagnosis of oxalate concentration in plasma and urine. Finally, this review provides information on the nutritional importance of these proteins in the human diet, as several members are known to be allergenic, a feature related to their thermal stability and evolutionary connection to the seed storage proteins, also members of the cupin superfamily.     

植物几丁质酶的结构与功能、分类及进化

近年来对几丁质酶的研究越来越深入,资料也愈来愈多。有的植物几丁质酶除具有几丁质酶活性,还具有其它的活性。典型的几丁质酶由N_端信号区、催化区和C_端延伸区组成,有的还有几丁质结合域。各功能域具有各自的功能。对植物几丁质酶的分类已经过多次改进,目前公认的是分成4组9个亚组。有证据表明植物几丁质酶在进化过程中有遗传转座现象,但具体进化过程还有待进一步确证。对几丁质酶与其它一些蛋白的关系的了解有助于理解几丁质酶的起源和进化。由于几丁质酶具有独特的抗真菌特性,因而几丁质酶基因成为目前抗真菌基因工程研究的热点之一。     

植物几丁质酶的结构与功能、分类及进化

近年来对几丁质酶的研究越来越深入,资料也愈来愈多,有的植物几丁质酶除具有几丁质酶活性,还具有其它的活性,典型的几丁质酶由－N－端信号区,催化区和C－端延伸区组成,有的还有几丁质结合域,各项能域具有各自的功能,对植物几丁质酶的分类已经过多次改进,目前公认的分成4组9个亚组,有证据表明植物几丁质酶在进化过程中有遗传转座现象,但具有进化过程还有待进一步确证,对几丁质酶与其它一些蛋白的关系的了解有助于理解几丁质酶的起源和进化,由于几丁质酶具有独特的抗真菌特性,因而几丁质酶基因成为目前抗真菌基因工程研究的热之一。     

The Structure, Function, and Evolution of a Regional Industrial Ecosystem

A framework has been developed to assess the structure, function, and evolution of a regional industrial ecosystem that integrates insights from industrial ecology and economic geography dimensions with complex systems theory. The framework highlights the multilayered landscape of natural ecosystem functions, economic transactions, policy contexts, and social interactions in which interfirm collaboration evolves. Its application to a single case study on the island of Puerto Rico revealed changes in the system's institutional context, its resource flows, and the composition of its industrial community. It illustrated that external forces and interactions among actors at multiple levels can cause permanent changes—but not necessarily system collapse—as policy choices and interfirm cooperation can be used to organize resources in ways that retain system functionality.     

Homepeptide Repeats:Implications for Protein Structure,Function and Evolution

Analysis of protein sequences from Mycobacterium tuberculosis H37Rv(Mtb H37Rv) was performed to identify homopeptide repeatcontaining proteins(HRCPs).Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism.Furthermore,these homopeptide repeats might play some specific roles in protein-protein interaction.Repeat length differences among Bacteria,Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms.From the results,it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes.In addition,there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species.Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded.Thus,homopeptide repeat may have structural,functional and evolutionary implications on proteins.     

Structure,Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA

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杆状病毒IAP基因的结构、功能及其进化

杆状病毒的IAP(inh ib itor of apoptosis prote in)基因是最早鉴定的IAP家族基因,具有B IR和R ING结构域特征,与杆状病毒P35基因有相似抗细胞凋亡功能,但在结构和作用机制上存在差异。系统分析表明,杆状病毒IAP基因可能是病毒与鳞翅目昆虫在长期的进化过程中从宿主基因组中获得的。     

高等植物光敏色素的分子结构、生理功能和进化特征

光敏色素是植物感受外界环境变化的最重要光受体之一,对红光和远红外光非常敏感。本文综述了光敏色素的分子结构、它所包含的结构域和相应功能以及植物各主要类群中光敏色素基因家族的成员组成与进化关系;重点在分子水平上介绍了光敏色素的生理功能与作用机制。最后,基于最新的研究进展提出了将来的研究方向。     

高等植物光敏色素的分子结构、生理功能和进化特征

光敏色素是植物感受外界环境变化的最重要光受体之一, 对红光和远红外光非常敏感。本文综述了光敏色素的分子结构、它所包含的结构域和相应功能以及植物各主要类群中光敏色素基因家族的成员组成与进化关系; 重点在分子水平上介绍了光敏色素的生理功能与作用机制。最后, 基于最新的研究进展提出了将来的研究方向。     

Structure, Function, and Evolution of the Crimean-Congo Hemorrhagic Fever Virus Nucleocapsid Protein

Crimean-Congo hemorrhagic fever virus (CCHFV) is an emerging tick-borne virus of the Bunyaviridae family that is responsible for a fatal human disease for which preventative or therapeutic measures do not exist. We solved the crystal structure of the CCHFV strain Baghdad-12 nucleocapsid protein (N), a potential therapeutic target, at a resolution of 2.1 Å. N comprises a large globular domain composed of both N- and C-terminal sequences, likely involved in RNA binding, and a protruding arm domain with a conserved DEVD caspase-3 cleavage site at its apex. Alignment of our structure with that of the recently reported N protein from strain YL04057 shows a close correspondence of all folds but significant transposition of the arm through a rotation of 180 degrees and a translation of 40 Å. These observations suggest a structural flexibility that may provide the basis for switching between alternative N protein conformations during important functions such as RNA binding and oligomerization. Our structure reveals surfaces likely involved in RNA binding and oligomerization, and functionally critical residues within these domains were identified using a minigenome system able to recapitulate CCHFV-specific RNA synthesis in cells. Caspase-3 cleaves the polypeptide chain at the exposed DEVD motif; however, the cleaved N protein remains an intact unit, likely due to the intimate association of N- and C-terminal fragments in the globular domain. Structural alignment with existing N proteins reveals that the closest CCHFV relative is not another bunyavirus but the arenavirus Lassa virus instead, suggesting that current segmented negative-strand RNA virus taxonomy may need revision.     

The Ribosomal Peptidyl Transferase Center: Structure,Function, Evolution,Inhibition

ABSTRACT

The ribosomal peptidyl transferase center (PTC) resides in the large ribosomal subunit and catalyzes the two principal chemical reactions of protein synthesis: peptide bond formation and peptide release. The catalytic mechanisms employed and their inhibition by antibiotics have been in the focus of molecular and structural biologists for decades. With the elucidation of atomic structures of the large ribosomal subunit at the dawn of the new millennium, these questions gained a new level of molecular significance. The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme. This places the ribosome on the list of naturally occurring riboyzmes that outlived the transition from the pre-biotic RNA World to contemporary biology. Biochemical, genetic and structural evidence highlight the role of the ribosome as an entropic catalyst that accelerates peptide bond formation primarily by substrate positioning. At the same time, peptide release should more strongly depend on chemical catalysis likely involving an rRNA group of the PTC. The PTC is characterized by the most pronounced accumulation of universally conserved rRNA nucleotides in the entire ribosome. Thus, it came as a surprise that recent findings revealed an unexpected high level of variation in the mode of antibiotic binding to the PTC of ribosomes from different organisms.     

Enigmatic Distribution,Evolution, and Function of Inteins

Inteins are mobile genetic elements capable of self-splicing post-translationally. They exist in all three domains of life including in viruses and bacteriophage, where they have a sporadic distribution even among very closely related species. In this review, we address this anomalous distribution from the point of view of the evolution of the host species as well as the intrinsic features of the inteins that contribute to their genetic mobility. We also discuss the incidence of inteins in functionally important sites of their host proteins. Finally, we describe instances of conditional protein splicing. These latter observations lead us to the hypothesis that some inteins have adapted to become sensors that play regulatory roles within their host protein, to the advantage of the organism in which they reside.     

植物抗病基因结构、功能及其进化机制研究进展

植物与病原菌在长期的共进化和相互选择的过程中,逐渐形成了组织障碍、非寄主抗性和小种专化抗性等有效的防御机制。小种专化抗性(基因对基因抗性)主要是由植物抗病基因识别相应的病原菌无毒基因并激活植物体内抗病信号进而抵御病原菌的侵染。从目前已克隆的 70 多个抗病基因来看,它们在结构上具有高度保守性,主要包括核苷酸结合位点(NBS),亮氨酸重复结构(LRR), 蛋白激酶结构域(PK), 果蝇蛋白 Toll 和哺乳动物蛋白质白细胞介素 1 受体[interleukin(IL)-1 receptor]类似结构域(TIR), 双螺旋结构(CC)或亮氨酸拉链(LZ)和跨膜结构域(TM)等,其在抗病基因与病原菌无毒(效应)蛋白互作以及植物内部免疫信号传导中起着重要的作用。同时,抗病基因又通过基因复制、遗传重组等进化机制形成多基因家族,为植物抗病的专化性和多样性提供了重要的遗传基础。本文主要讨论了近来已克隆抗病基因的结构特征、功能以及抗病基因进化机制研究的进展。     

Rab蛋白的结构、功能及进化

Rab蛋白是小分子GTP结合蛋白家族(small GTP-binding proteins)中最大的亚家族,大约由200个氨基酸组成,由保守的G结构域与高度可变的N端和C端组成。Rab蛋白作为细胞内囊泡运输的分子开关,与其上游调控子和下游特定的效应子相互作用,并与GTP的结合和水解过程相偶联,在囊泡运输的不同阶段发挥作用。对不同Rab蛋白调控囊泡运输的研究有利干全面理解细胞内各类囊泡定向运输的分子动力学机制。     

ATP Synthases With Novel Rotor Subunits: New Insights into Structure,Function and Evolution of ATPases

ATPases with unusual membrane-embedded rotor subunits were found in both F₁F₀ and A₁A₀ ATP synthases. The rotor subunit c of A₁A₀ ATPases is, in most cases, similar to subunit c from F₀. Surprisingly, multiplied c subunits with four, six, or even 26 transmembrane spans have been found in some archaea and these multiplication events were sometimes accompanied by loss of the ion-translocating group. Nevertheless, these enzymes are still active as ATP synthases. A duplicated c subunit with only one ion-translocating group was found along with “normal” F₀ c subunits in the Na⁺ F₁F₀ ATP synthase of the bacterium Acetobacterium woodii. These extraordinary features and exceptional structural and functional variability in the rotor of ATP synthases may have arisen as an adaptation to different cellular needs and the extreme physicochemical conditions in the early history of life.     

Ligand Binding Site Structure Influences the Evolution of Protein Complex Function and Topology

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