共查询到20条相似文献,搜索用时 31 毫秒
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2.
Paul Francis Morris Laura Rose Schlosser Katherine Diane Onasch Tom Wittenschlaeger Ryan Austin Nicholas Provart 《PloS one》2009,4(7)
Complex enzymes with multiple catalytic activities are hypothesized to have evolved from more primitive precursors. Global analysis of the Phytophthora sojae genome using conservative criteria for evaluation of complex proteins identified 273 novel multifunctional proteins that were also conserved in P. ramorum. Each of these proteins contains combinations of protein motifs that are not present in bacterial, plant, animal, or fungal genomes. A subset of these proteins were also identified in the two diatom genomes, but the majority of these proteins have formed after the split between diatoms and oomycetes. Documentation of multiple cases of domain fusions that are common to both oomycetes and diatom genomes lends additional support for the hypothesis that oomycetes and diatoms are monophyletic. Bifunctional proteins that catalyze two steps in a metabolic pathway can be used to infer the interaction of orthologous proteins that exist as separate entities in other genomes. We postulated that the novel multifunctional proteins of oomycetes could function as potential Rosetta Stones to identify interacting proteins of conserved metabolic and regulatory networks in other eukaryotic genomes. However ortholog analysis of each domain within our set of 273 multifunctional proteins against 39 sequenced bacterial and eukaryotic genomes, identified only 18 candidate Rosetta Stone proteins. Thus the majority of multifunctional proteins are not Rosetta Stones, but they may nonetheless be useful in identifying novel metabolic and regulatory networks in oomycetes. Phylogenetic analysis of all the enzymes in three pathways with one or more novel multifunctional proteins was conducted to determine the probable origins of individual enzymes. These analyses revealed multiple examples of horizontal transfer from both bacterial genomes and the photosynthetic endosymbiont in the ancestral genome of Stramenopiles. The complexity of the phylogenetic origins of these metabolic pathways and the paucity of Rosetta Stones relative to the total number of multifunctional proteins suggests that the proteome of oomycetes has few features in common with other Kingdoms. 相似文献
3.
Several representatives of the Crenarchaeal branch of the Archaea contain highly abundant, small, positively charged proteins
exemplified by the Sso7d protein from Sulfolobus solfataricus. These proteins bind to DNA in a non-sequence-specific manner. Using publicly available genomic sequence information, we
identified a second class of small Crenarchaeal DNA-binding proteins represented by the Pyrobaculum aerophilum open reading frame 3192–encoded (Pae3192) protein and its paralogs. We investigated the biochemical properties of the Pae3192
protein and an orthologous protein (Ape1322b) from Aeropyrum pernix in side-by-side experiments with the Sso7d protein. We demonstrate that the recombinant Ape1322b, Pae3192 and Sso7d proteins
bind to DNA and that the DNA-protein complexes formed are slightly different for each protein. We show that like Sso7d, Pae3192
constrains negative supercoils in DNA. In addition, we show that all three proteins raise the melting temperature of duplex
DNA upon binding. Finally, we present the equilibrium affinity constants and kinetic association constants of each protein
for single-stranded and double-stranded DNA. 相似文献
4.
Hervé Thiellement Marc Seguin Nasser Bahrman Michel Zivy 《Journal of molecular evolution》1989,29(1):89-94
Summary Two-dimensional gel electrophoresis of seedling proteins has been undertaken on diploid representatives of the A, S, and DTriticum genomes. The 457 reproducible spots of the hexaploid Chinese Spring were taken into account in the comparisons. More than 82% of the hexaploid spots were found among the representatives of each of the three genomes. Thus, it was proposed that the homoeologous structural loci, on the three homoeologous genomes, can be present in the same allelic forms and that from 72% to 86% of the spots of the hexaploid pattern are in two or three doses. The dendrogram, deduced from the similarity indices computed between the 16 diploid accessions, was very consistent with our present knowledge of the genetic relationships in theTriticum genus. This result, in addition to previous ones, shows that the comparison of two-dimensional protein patterns represents a novel experimental approach for studying the phylogenetic relationships in theTriticinae. 相似文献
5.
The compositional distributions of large DNA fragments reflect those of the isochores that make up vertebrate genomes and
can provide novel phylogenetic insights in the case of mammalian genomes (see Sabeur et al. 1993). This approach has been
complemented here by an analysis of the compositional patterns of coding sequences and their codon positions (which also reflect
the isochore pattern) and by a comparison of the base compositions of codon positions from homologous genes in a number of
pairs of species. The results obtained using these two approaches support the existence of a general compositional pattern
for mammalian genomes and of a distinct pattern for Myomorpha. The other two “special” patterns identified in a megachiropteran
and in pangolin could not be tested here.
Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992 相似文献
6.
The small heat shock proteins (sHSPs) are a diverse family of molecular chaperones. It is well established that these proteins
are crucial components of the plant heat shock response. They also have important roles in other stress responses and in normal
development. We have conducted a comparative sequence analysis of the sHSPs in three complete angiosperms genomes: Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa. Our phylogenetic analysis has identified four additional plant sHSP subfamilies and thus has increased the number of plant
sHSP subfamilies from 7 to 11. We have also identified a number of novel sHSP genes in each genome that lack close homologs
in other genomes. Using publicly available gene expression data and predicted secondary structures, we have determined that
the sHSPs in plants are far more diverse in sequence, expression profile, and in structure than had been previously known.
Some of the newly identified subfamilies are not stress regulated, may not posses the highly conserved large oligomer structure,
and may not even function as molecular chaperones. We found no consistent evolutionary patterns across the three species studied.
For example, gene conversion was found among the sHSPs in O. sativa but not in A. thaliana or P. trichocarpa. Among the three species, P. trichocarpa had the most sHSPs. This was due to an expansion of the cytosolic I sHSPs that was not seen in the other two species. Our
analysis indicates that the sHSPs are a dynamic protein family in angiosperms with unexpected levels of diversity.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
7.
Marielle Merlino Philippe Leroy Christophe Chambon Gérard Branlard 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(7):1321-1337
Albumins and globulins of wheat endosperm represent 20% of total kernel protein. They are soluble proteins, mainly enzymes
and proteins involved in cell functions. Two-dimensional gel immobiline electrophoresis (2DE) (pH 4-7) × SDS-Page revealed
around 2,250 spots. Ninety percent of the spots were common between the very distantly related cultivars ‘Opata 85’ and ‘Synthetic
W7984’, the two parents of the International Triticeae Mapping Initiative (ITMI) progeny. ‘Opata’ had 130 specific spots while
‘Synthetic’ had 96. 2DE and image analysis of the soluble proteins present in 112 recombinant inbred lines of the F9-mapped
ITMI progeny enabled 120 unbiased segregating spots to be mapped on 21 wheat (Triticum aestivum L. em. Thell) chromosomes. After trypsic digestion, mapped spots were subjected to MALDI-Tof or tandem mass spectrometry for
protein identification by database mining. Among the ‘Opata’ and ‘Synthetic’ spots identified, many enzymes have already been
mapped in the barley and rice genomes. Multigene families of Heat Shock Proteins, beta-amylases, UDP-glucose pyrophosphorylases,
peroxydases and thioredoxins were successfully identified. Although other proteins remain to be identified, some differences
were found in the number of segregating proteins involved in response to stress: 11 proteins found in the modern selected
cultivar ‘Opata 85’ as compared to 4 in the new hexaploid `Synthetic W7984’. In addition, ‘Opata’ and ‘Synthetic’ differed
in the number of proteins involved in protein folding (2 and 10, respectively). The usefulness of the mapped enzymes for future
research on seed composition and characteristics is discussed.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
8.
M. Podnar W. Pinsker W. Mayer 《Journal of Zoological Systematics and Evolutionary Research》2009,47(1):35-41
Complete mitochondrial (mt) genomes were sequenced from representatives of three lacertid lizards: Podarcis siculus, Podarcis muralis and Phoenicolacerta kulzeri. In all three genomes the arrangement of the 22 tRNAs, the two rRNAs and the 13 protein‐coding genes conforms to the common vertebrate arrangement. The phylogenetic position of Lacertidae within the order Squamata was determined through sequence analyses based on large sections of complete mt genomes. The number of nucleotide sites used for tree construction was 9234 when outgroup taxa were included, and 10 499 when only Squamata were compared. The phylogenetic analyses confirmed the sister group relationship between Lacertidae and Amphisbaenia as previously proposed on the basis of molecular data. Additionally, Bayesian analysis revealed a well supported clade comprising (Gekkonidae (Lacertidae + Amphisbaenia)), which is not in accordance with the traditional morphological view and most of the previous molecular studies. It confirms, however, the close relationship between Gekkonidae and Amphisbaenia as revealed in a recent study based on complete mt genomes from a smaller number of taxa. Intra‐ and intergeneric sequence comparisons of six commonly used marker genes showed rather high levels of divergence within the Lacertidae. In the intrageneric comparison the control region proved to be considerably more conserved than the protein coding genes. 相似文献
9.
Hess WR Rocap G Ting CS Larimer F Stilwagen S Lamerdin J Chisholm SW 《Photosynthesis research》2001,70(1):53-71
Within the vast oceanic gyres, a significant fraction of the total chlorophyll belongs to the light-harvesting antenna systems
of a single genus, Prochlorococcus. This organism, discovered only about 10 years ago, is an extremely small, Chl b-containing cyanobacterium that sometimes constitutes up to 50% of the photosynthetic biomass in the oceans. Various Prochlorococcus strains are known to have significantly different conditions for optimal growth and survival. Strains which dominate the
surface waters, for example, have an irradiance optimum for photosynthesis of 200 μmol photons m−2 s−1, whereas those that dominate the deeper waters photosynthesize optimally at 30–50 μmol photons m−2 s−1. These high and low light adapted ‘ecotypes’ are very closely related — less than 3% divergent in their 16S rRNA sequences
— inviting speculation as to what features of their photosynthetic mechanisms might account for the differences in photosynthetic
performance. Here, we compare information obtained from the complete genome sequences of two Prochlorococcus strains, with special emphasis on genes for the photosynthetic apparatus. These two strains, Prochlorococcus MED4 and MIT 9313, are representatives of high- and low-light adapted ecotypes, characterized by their low or high Chl b/a ratio, respectively. Both genomes appear to be significantly smaller (1700 and 2400 kbp) than those of other cyanobacteria,
and the low-light-adapted strain has significantly more genes than its high light counterpart. In keeping with their comparative
light-dependent physiologies, MED4 has many more genes encoding putative high-light-inducible proteins (HLIP) and photolyases
to repair UV-induced DNA damage, whereas MIT 9313 possesses more genes associated with the photosynthetic apparatus. These
include two pcb genes encoding Chl-binding proteins and a second copy of the gene psbA, encoding the Photosystem II reaction center protein D1. In addition, MIT 9313 contains a gene cluster to produce chromophorylated
phycoerythrin. The latter represents an intermediate form between the phycobiliproteins of non-Chl b containing cyanobacteria and an extremely modified β phycoerythrin as the sole derivative of phycobiliproteins still present
in MED4. Intriguing features found in both Prochlorococcus strains include a gene cluster for Rubisco and carboxysomal proteins that is likely of non-cyanobacterial origin and two
genes for a putative
and β lycopene cyclase, respectively, explaining how Prochlorococcus may synthesize the α branch of carotenoids that are common in green organisms but not in other cyanobacteria.
This revised version was published online in June 2006 with corrections to the Cover Date. 相似文献
10.
The complete mitochondrial genomes of five tiger samples from three subspecies (P. t. sumatrae, P. t. altica, and P. t. tigris) were successfully obtained by using 26 specifically designed Panthera-specific primer sets. The genome organization and gene arrangement of the five tiger samples were similar to each other;
however polymorphic tandem repeat sequences were observed in the control region (CR). This led to a difference in the genome
lengths obtained from these five samples with an average size of 16,994 bp for the five tiger mitochondrial genomes. The nucleotide
base composition was on average as follows: A, 31.8%; T, 27.0%; C, 26.6%; G, 14.6% and exhibited compositional asymmetry.
Most of tiger mitochondrial genome characteristics are similar to those of other common vertebrate species; however, some
distinctive features were observed in the CR. First, the repetitive sequence 2 (RS 2) contained two repeat units of 80 bp
and the first 15 bp of what would be the third repeat motif. The repetitive sequence 3 (RS 3) contained 47–50 repeat motifs
of a shorter 8 bp (ACGTAYAC)n. Second, length heteroplasmy polycystosine (poly-C) stretches was observed at the end of the HV I locus in all tiger samples. 相似文献
11.
Pseudomonas syringae isolate BR2R produces tabtoxin, a β-lactam-containing antibiotic, and the causative agent of wildfire disease of green bean
(Phaseolus vulgaris). β-Lactamase production has been suggested as the mechanism that protects P. syringae from tabtoxin. We sought to determine whether the organism produces β-lactamase and whether the enzyme plays a role in protection
from this antibiotic. P. syringae and mutants defective in tabtoxin production and resistance produce β-lactamase. Three distinct β-lactamases with molecular
weights of 41,000 were identified. The isoelectric points of the proteins were 6.1, 6.8, and 9.2. The enzymes preferentially
hydrolyze cephalosporin. This investigation demonstrates that the organism produces multiple β-lactamases and describes characteristics
of the proteins. 相似文献
12.
Sequence analysis corresponding to the PPE and PE proteins in<Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> and other genomes 总被引:2,自引:0,他引:2
Amino acid sequence analysis corresponding to the PPE proteins in H37Rv and CDC 1551 strains of theMycobacterium tuberculosis genomes resulted in the identification of a previously uncharacterized 225 amino acid-residue common region in 22 proteins.
The pairwise sequence identities were as low as 18%. Conservation of amino acid residues was observed at fifteen positions
that were distributed over the whole length of the region. The secondary structure corresponding to this region is predicted
to be a mixture of a-helices and β-strands. Although the function is not known, proteins with this region specific to mycobacterial
species may be associated with a common function. We further observed another group of 20 PPE proteins corresponding to the
conserved C-terminal region comprising 44 amino acid residues with GFxGT and PxxPxxW sequence motifs. This region is preceded
by a hydrophobic region, comprising 40–100 amino acid residues, that is flanked by charged amino acid residues. Identification
of conserved regions described above may be useful to detect related proteins from other genomes and assist the design of
suitable experiments to test their corresponding functions. Amino acid sequence analysis corresponding to the PE proteins
resulted in the identification of tandem repeats comprising 41-43 amino acid residues in the C-terminal variable regions in
two PE proteins (Rv0978 and Rv0980). These correspond to the AB repeats that were first identified in some proteins of theMethanosarcina mazei genome, and were demonstrated as surface antigens. We observed the AB repeats also in several other proteins of hitherto
uncharacterized function inArchaea andBacteria genomes. Some of these proteins are also associated with another repeat called the C-repeat or the PKD-domain comprising
85 amino acid residues. The secondary structure corresponding to the AB repeat is predicted mainly as 4 β-strands. We suggest
that proteins with AB repeats inMycobacterium tuberculosis and other genomes may be associated as surface antigens. TheM. leprae genome, however, does not contain either the AB or C-repeats and different proteins may therefore be recruited as surface
antigens in theM. leprae genome compared to theM. tuberculosis genome. 相似文献
13.
Disulfide reductases of host-colonising bacteria are involved in the expression of virulence factors, resistance to drugs,
and elimination of toxic compounds. Large-scale genome analyses of 281 prokaryotes identified CXXC and CXXC-derived motifs
in each microorganism. The total number of these motifs showed correlations with genome size and oxygen tolerance of the prokaryotes.
Specific bioinformatic analyses served to identify putative disulfide reductases in the Campylobacterales Campylobacter jejuni, Helicobacter pylori, Wolinella succinogenes and Arcobacter butzleri which colonise the gastrointestinal tract of higher animals. Three filters applied to the genomes of these species yielded
35, 25, 28 and 34 genes, respectively, encoding proteins with the characteristics of disulfide reductases. Ten proteins were
common to the four species, including four belonging to the thioredoxin system. The presence of thioredoxin reductase activities
was detected in the four bacterial species by observing dithiobis-2-nitrobenzoic acid reduction with β-nicotinamide adenine
dinucleotide phosphate as cofactor. Phylogenetic analyses of the thioredoxin reductases TrxB1 and TrxB2 of the four Campylobacterales were performed. Their TrxB1 proteins were more closely related to those of Firmicutes than to the corresponding proteins of other Proteobacteria. The
Campylobacterales TrxB2 proteins were closer to glutathione reductases of other organisms than to their respective TrxB1 proteins. The phylogenetic features of the Campylobacterales thioredoxin reductases suggested a special role for these enzymes
in the physiology of these bacteria.
Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
14.
《Expert review of proteomics》2013,10(5):573-591
Neisseria meningitidis (meningococcus) is a major causative organism of meningitis and sepsis and Neisseria gonorrhoeae (gonococcus) is the causative organism of the sexually transmitted disease gonorrhea. Infections caused by meningococci are vaccine-preventable, whereas gonococcal vaccine research and development has languished for decades and the correlates of protection are still largely unknown. In the past two decades, complementary ‘omic’ platforms have been developed to interrogate Neisseria genomes and gene products. Proteomic techniques applied to whole Neisseria bacteria, outer membranes and outer membrane vesicle vaccines have generated protein maps and also allowed the examination of environmental stresses on protein expression. In particular, immuno-proteomics has identified proteins whose expression is correlated with the development of human natural immunity to meningococcal infection and colonization and following vaccination. Neisseria proteomic techniques have produced a catalog of potential vaccine antigens and investigating the functional and biological properties of these proteins could finally provide ‘universal’ Neisseria vaccines. 相似文献
15.
Shiri Freilich Leon Goldovsky Assaf Gottlieb Eric Blanc Sophia Tsoka Christos A Ouzounis 《BMC bioinformatics》2009,10(1):355
Background
Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present rank-BLAST, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database. 相似文献16.
Rapid evolution of snake venom genes by positive selection has been reported previously but key features of this process such
as the targets of selection, rates of gene turnover, and functional diversity of toxins generated remain unclear. This is
especially true for closely related species with divergent diets. We describe the evolution of PLA2 gene sequences isolated from genomic DNA from four taxa of Sistrurus rattlesnakes which feed on different prey. We identified four to seven distinct PLA2 sequences in each taxon and phylogenetic analyses suggest that these sequences represent a rapidly evolving gene family consisting
of both paralogous and homologous loci with high rates of gene gain and loss. Strong positive selection was implicated as
a driving force in the evolution of these protein coding sequences. Exons coding for amino acids that make up mature proteins
have levels of variation two to three times greater than those of the surrounding noncoding intronic sequences. Maximum likelihood
models of coding sequence evolution reveal that a high proportion (∼30%) of all codons in the mature protein fall into a class
of codons with an estimated d
N
/d
S
(ω) ratio of at least 2.8. An analysis of selection on individual codons identified nine residues as being under strong (p < 0.01) positive selection, with a disproportionately high proportion of these residues found in two functional regions of
the PLA2 protein (surface residues and putative anticoagulant region). This is direct evidence that diversifying selection has led
to high levels of functional diversity due to structural differences in proteins among these snakes. Overall, our results
demonstrate that both gene gain and loss and protein sequence evolution via positive selection are important evolutionary
forces driving adaptive divergence in venom proteins in closely related species of venomous snakes. 相似文献
17.
O. S. Bychenko L. V. Sukhanova T. L. Azhikina E. D. Sverdlov 《Russian Journal of Bioorganic Chemistry》2009,35(6):766-768
Two representatives of Baikal ciscoes—lake cisco and omul—diverged from a common ancestor as recently as 10–20 thousand years
ago. We have found an increasing expression level of DTSsa4 Tc1-like DNA transposons in cisco and omul brains. The mapping
of the sequences of these transposons from Salmo salar and Danio rerio genomes has shown that in some cases, these transposons are located in the 5′ and 3′ regions, as well as in the promoter
regions of various genes. Probably, Tc1-like transposons affect the activity of neighboring genes, providing the adaptive
divergence of the cisco population. 相似文献
18.
With recent breakthroughs in experimental microbiology making it possible to synthesize and implant an entire genome to create a living cell, the challenge of constructing a working blueprint for the first truly minimal synthetic organism is more important than ever. Here we review the significant progress made in the design and creation of a minimal organism. We discuss how comparative genomes, gene essentiality data, naturally small genomes, and metabolic modeling are all being applied to produce a catalogue of the biological functions essential for life. We compare the minimal gene sets from three published sources with functions identified in 13 existing gene essentiality datasets. We examine how genome-scale metabolic models have been applied to design a minimal metabolism for growth in simple and complex media. Additionally, we survey the progress of efforts to construct a minimal organism, either through implementation of combinatorial deletions in Bacillus subtilis and Escherichia coli or through the synthesis and implantation of synthetic genomes. 相似文献
19.
Christine P. Piotte Airlie K. Hunter Craig J. Marshall Murray R. Grigor 《Journal of molecular evolution》1998,46(3):361-369
Three proteins have been identified in the milk of the common brush tail possum, Trichosurus vulpecula that from sequence analysis are members of the lipocalin family. They include β-lactoglobulin, which appears to have two
forms; a homologue to the late-lactation protein found in tammar, Macropus eugenii; milk; and a novel protein termed trichosurin. Whereas β-lactoglobulin and trichosurin are both expressed throughout lactation, the late-lactation protein is not detected
in samples taken before days 100–110 of lactation. The cDNAs encoding each of these proteins have been isolated from cDNA
libraries prepared using possum mammary mRNA and sequenced. Phylogenetic analysis showed that the T. vulpeculaβ-lactoglobulin, along with two other macropod β-lactoglobulins, forms a subclass of β-lactoglobulins distinct from those
for eutherian mammals; both marsupial late-lactation proteins appear to have similarities to a family of odorant-binding proteins,
whereas trichosurin has similarities to the major urinary proteins of rodents.
Received: 28 October 1996 / Accepted: 19 May 1997 相似文献
20.
The Pumilio protein is the founding member of the PUF family of RNA-binding proteins, which contains 8 repeat Puf domains
and plays important roles during embryogenesis and post-embryogenesis by binding the Nanos response element (NRE) of specific
target genes in eukaryotes. In addition, many other proteins containing the Puf domain were identified but with different
functions from the Pumilio protein in various species. Taking advantage of the newly assembled genome sequences, in this study
we performed a genome-wide analysis of PUF genes in silkworm and other 27 species. In the silkworm, three PUF genes were identified, named Bmpumilio, Bmpenguin and Bmnop by homology analysis. In fungi and animals, four evolutionarily conservational PUF gene families were identified, Group-A, -B, -C and -D. While Group-A, -C, and -D are present in all fungi and animals, Group-B
was only identified in fungi. Interestingly, the number and features of the Puf domains are distinct in each group, suggesting
different roles for these proteins in every group. The EST and microarray data showed that the mRNA of the three PUF genes can be widely detected in all tissues of the silkworm. Our results provide some new insights into the functions and
evolutionary characteristics of PUF proteins. 相似文献