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101.
102.
The increasing availability of sequenced genomes enables the reconstruction of the evolutionary history of large protein complexes. Here, we trace the evolution of NADH:ubiquinone oxidoreductase (Complex I), which has increased in size, by so-called supernumary subunits, from 14 subunits in the bacteria to 30 in the plants and algae, 37 in the fungi and 46 in the mammals. Using a combination of pair-wise and profile-based sequence comparisons at the levels of proteins and the DNA of the sequenced eukaryotic genomes, combined with phylogenetic analyses to establish orthology relationships, we were able to (1) trace the origin of six of the supernumerary subunits to the alpha-proteobacterial ancestor of the mitochondria, (2) detect previously unidentified homology relations between subunits from fungi and mammals, (3) detect previously unidentified subunits in the genomes of several species and (4) document several cases of gene duplications among supernumerary subunits in the eukaryotes. One of these, a duplication of N7BM (B17.2), is particularly interesting as it has been lost from genomes that have also lost Complex I proteins, making it a candidate for a Complex I interacting protein. A parsimonious reconstruction of eukaryotic Complex I evolution shows an initial increase in size that predates the separation of plants, fungi and metazoa, followed by a gradual adding and incidental losses of subunits in the various evolutionary lineages. This evolutionary scenario is in contrast to that for Complex I in the prokaryotes, for which the combination of several separate, and previously independently functioning modules into a single complex has been proposed. 相似文献
103.
The correlation between manganese deficiency, loss of mitochondrial respiratory chain NADH: ubiquinone oxidoreductase (complex I) activity and citric acid overproduction in the Aspergillus niger strain B 60 was analysed. With increasing manganese-supplementation of the production medium the loss of complex I activity and the production of citric acid was reduced. Addition of manganese during growth stopped further loss of complex I activity and further increase of citric acid production. A possible causality between complex I deficiency and citric acid overproduction is discussed. 相似文献
104.
猪胸膜肺炎放线杆菌flic蛋白二级结构与B细胞表位预测 总被引:2,自引:0,他引:2
目的:预测和分析猪胸膜肺炎放线杆菌(Actionobacillus pleuropneumoniae,APP)鞭毛蛋白(flic)的二级结构和B细胞表位.方法:利用生物信息学方法对flic基因推导的氨基酸序列进行结构特征和B细胞表位预测分析.结果:flic蛋白为非稳定型脂蛋白,含有2个酪蛋白激酶Ⅱ磷酸化位点(39-42 SirD,164-167 SvkD)和3个蛋白质激酶C磷酸化位点(39-41 SiR,161-163 TsR、164-166 SvK).该蛋白无信号肽,在21Ala~38Ala处存在跨膜区的可能性最大.fljc蛋白的二级结构主要由无规卷曲区域、α-螺旋和β-折叠组成,而形成较少的转角结构.该蛋白的B细胞表位可能位于55~61和152~158区段内或其附近区域.结论:预测结果将有助于确定file蛋白的B细胞表位,为进一步研究flic基因功能及研制APP基因工程疫苗提供参考. 相似文献
105.
Barik S 《Journal of biosciences》2004,29(3):261-273
The significance of the intron-exon structure of genes is a mystery. As eukaryotic proteins are made up of modular functional
domains, each exon was suspected to encode some form of module; however, the definition of a module remained vague. Comparison
of pre-mRNA splice junctions with the three-dimensional architecture of its protein product from different eukaryotes revealed
that the junctions were far less likely to occur inside the α-helices and Β-strands of proteins than within the more flexible
linker regions (‘turns’ and ‘loops’) connecting them. The splice junctions were equally distributed in the different types
of linkers and throughout the linker sequence, although a slight preference for the central region of the linker was observed.
The avoidance of the α-helix and the (Β-strand by splice junctions suggests the existence of a selection pressure against
their disruption, perhaps underscoring the investment made by nature in building these intricate secondary structures. A corollary
is that the helix and the strand are the smallest integral architectural units of a protein and represent the minimal modules
in the evolution of protein structure. These results should find use in comparative genomics, designing of cloning strategies,
and in the mutual verification of genome sequences with protein structures. 相似文献
106.
Hirotaka Furukawa Marco Wieser Hiroshi Morita Tsuyoshi Sugio T. Nagasawa 《Archives of microbiology》1998,171(1):37-43
Pseudomonas fluorescens E118 was isolated from soil as an effective eugenol-degrading organism by a screening using eugenol as enrichment substrate.
The first enzyme involved in the degradation of eugenol in this organism, eugenol dehydrogenase, was purified after induction
by eugenol, and the purity of the enzyme was shown by SDS-PAGE and gel-permeation HLPC. The enzyme is a heterodimer that consists
of a 10-kDa cytochrome c and a 58-kDa subunit. The larger subunit presumably contains flavin, suggesting a flavocytochrome c structure and an electron transfer via flavin and cytochrome c during dehydrogenation. The activity of the purified enzyme depended on the addition of a final electron acceptor such as
phenazine methosulfate, 2,6-dichlorophenol-indophenol, cytochrome c, or potassium ferricyanide. The enzyme catalyzed the dehydrogenation of three different 4-hydroxybenzylic structures including
the conversion of eugenol to coniferyl alcohol, 4-alkylphenols to 1-(4-hydroxyphenyl)alcohols, and 4-hydroxybenzylalcohols
to the corresponding aldehydes. The catalytic and structural similarity between this enzyme and a Penicillium vanillyl-alcohol oxidase and 4-alkylphenol methylhydroxylases from several Pseudomonas species is discussed.
Received: 17 June 1998 / Accepted: 12 October 1998 相似文献
107.
Lack of seed dispersal can be an important obstacle to natural regeneration (NR) of degraded pastures in the humid tropics. Tree plantations can facilitate secondary forest succession by attracting seed dispersal agents from nearby forests. We studied seed rain and seed dispersal agents in 12–13 years old pure and mixed native tree plantations at La Selva Biological Station, Costa Rica from July to December 2004. Plantations of Balizia elegans (5,522), Dipteryx panamensis (2,263), and Jacaranda copaia (2,091) had the greatest total seed abundance; treatments with the least total seed abundance were Calophyllum brasiliense (56), nonplanted abandoned pasture control 2 (353), Mixed Species 2 (389), and control 1 (836). Plantations of J. copaia and Hyeronima alchorneoides had the greatest seed species richness density, whereas the lowest seed species richness was found in the control treatments. The NR plots had more seeds dispersed by wind, whereas in the plantations, the most important dispersal agents were birds and mammals. The most abundant seeds were those of Miconia spp. (14,492), Psychotria bracheata (2,252), and the Poaceae family (1,346), all species from early successional stages. Plantations of native species are effective in attracting seed dispersal agents and thus facilitating regeneration of degraded pasturelands in the region. 相似文献
108.
A probabilistic graphical model is proposed in order to detect the coevolution between different sites in biological sequences. The model extends the continuous-time Markov process of sequence substitution for single nucleic or amino acids and imposes general constraints regarding simultaneous changes on the substitution rate matrix. Given a multiple sequence alignment for each molecule of interest and a phylogenetic tree, the model can predict potential interactions within or between nucleic acids and proteins. Initial validation of the model is carried out using tRNA and 16S rRNA sequence data. The model accurately identifies the secondary interactions of tRNA as well as several known tertiary interactions. In addition, results on 16S rRNA data indicate this general and simple coevolutionary model outperforms several other parametric and nonparametric methods in predicting secondary interactions. Furthermore, the majority of the putative predictions exhibit either direct contact or proximity of the nucleotide pairs in the 3-dimensional structure of the Thermus thermophilus ribosomal small subunit. The results on RNA data suggest a general model of coevolution might be applied to other types of interactions between protein, DNA, and RNA molecules. 相似文献
109.
Jäger M Dendle M Fuller AA Kelly JW 《Protein science : a publication of the Protein Society》2007,16(10):2306-2313
Using the human Pin1 WW domain (hPin1 WW), we show that replacement of two nearest neighbor non-hydrogen-bonded residues on adjacent beta-strands with tryptophan (Trp) residues increases beta-sheet thermodynamic stability by 4.8 kJ mol(-1) at physiological temperature. One-dimensional NMR studies confirmed that introduction of the Trp-Trp pair does not globally perturb the structure of the triple-stranded beta-sheet, while circular dichroism studies suggest that the engineered cross-strand Trp-Trp pair adopts a side-chain conformation similar to that first reported for a designed "Trp-zipper" beta-hairpin peptide, wherein the indole side chains stack perpendicular to each other. Even though the mutated side chains in wild-type hPin1 WW are not conserved among WW domains and compose the beta-sheet surface opposite to that responsible for ligand binding, introduction of the cross-strand Trp-Trp pair effectively eliminates hPin1 WW function as assessed by the loss of binding affinity toward a natural peptide ligand. Maximizing both thermodynamic stability and the domain function of hPin1 WW by the above mentioned approach appears to be difficult, analogous to the situation with loop 1 optimization explored previously. That introduction of a non-hydrogen-bonded cross-strand Trp-Trp pair within the hPin1 WW domain eliminates function may provide a rationale for why this energetically favorable pairwise interaction has not yet been identified in WW domains or any other biologically evolved protein with known three-dimensional structure. 相似文献
110.
Sulfite-oxidizing enzyme activities were analyzed in cell-free extracts of aerobically grown cells of Acidianus ambivalens, an extremely thermophilic and chemolithoautotrophic archaeon. In the membrane and cytoplasmic fractions, two distinct enzyme
activities were found. In the membrane fraction, a sulfite:acceptor oxidoreductase activity was found [530 mU (mg protein)–1; apparent K
m for sulfite, 3.6 mM]. In the cytoplasmic fraction the following enzyme activities were found and are indicative of an oxidative
adenylylsulfate pathway: adenylylsulfate reductase [138 mU (mg protein)–1], adenylylsulfate:phosphate adenyltransferase [“ADP sulfurylase”; 86 mU (mg protein)–1], adenylate kinase [650 mU (mg protein)–1], and rhodanese [thiosulfate sulfur transferase, 9.2 mU (mg protein)–1]. In addition, 5′,5′′′-P1,P4-di(adenosine-5′) tetraphosphate (Ap4A) synthase and Ap4A pyrophosphohydrolase activities were detected.
Received: 17 August 1998 / Accepted: 29 April 1999 相似文献