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1.
Glyoxalase I (GlxI) is the first of two enzymes involved in the cellular detoxification of methylglyoxal. A recent search
of the National Center for Biotechnology Information (NCBI) databases with the protein sequence of Salmonella typhimurium GlxI identified two new hypothetical proteins with unassigned function. These two sequences, from Brassica oleracea and Sporobolus stapfianus, have significant sequence similarity to known GlxI sequences, suggesting that these two open reading frames encode for GlxI
in these plants. Interestingly, analysis of these two new sequences indicates that they code for a protein composed of two
fused monomers, a situation previously found solely in the yeast GlxI enzymes.
Received: 10 May 1997 / Accepted: 15 October 1997 相似文献
2.
Sowmya Raghavan Pradeep K. Burma Samir K. Brahmachari 《Journal of molecular evolution》1997,45(5):485-498
The complete genome of the baker's yeast S. cerevisiae was analyzed for the presence of polypurine/polypyrimidine (poly[pu/py]) repeats and their occurrences were classified on
the basis of their location within and outside open reading frames (ORFs). The analysis reveals that such sequence motifs
are present abundantly both in coding as well as noncoding regions. Clear positional preferences are seen when these tracts
occur in noncoding regions. These motifs appear to occur predominantly at a unit nucleosomal length both upstream and downstream
of ORFs. Moreover, there is a biased distribution of polypurines in the coding strands when these motifs occur within open
reading frames. The significance of the biased distribution is discussed with reference to the occurrence of these motifs
in other known mRNA sequences and expressed sequence tags. A model for cis regulation of gene expression is proposed based on the ability of these motifs to form an intermolecular triple helix structure
when present within the coding region and/or to modulate nucleosome positioning via enhanced histone affinity when present
outside coding regions.
Received: 14 November 1996 / Accepted: 7 May 1997 相似文献
3.
The genomic organization of the hsp83 gene of Drosophila auraria, a far-eastern endemic species belonging to the montium subgroup of the melanogaster species group, is presented here. Based on in situ hybridization on polytene chromosomes, cDNA and genomic clone mapping,
nucleotide sequencing, and genomic Southern analysis, hsp83 is shown to be present as a single-copy gene at locus 64B on the 3L chromosome arm in D. auraria. This gene is organized into two exons separated by a 929-bp intron. The first exon represents the mRNA leader sequence and
is not translated, while the coding region, having a length of 2,151 bp, is solely included in the second exon. Nucleotide
sequence comparisons of D. auraria hsp83 with homologous sequences from other organisms show high conservation of the coding region (88–92% identity) in the genus
Drosophila, in addition to the conserved genomic organization of two-exons–one-intron, of comparable size and arrangement. A phylogenetic
tree based on the protein sequences of homologous genes from representative organisms is in accord with the accredited phylogenetic
position of D. auraria. In the hsp83 gene region, a second case of long antiparallel coupled open reading frames (LAC ORFs) for this species was found. The antiparallel
to the hsp83 gene ORF is 1,554 bases long, while the two ORFs overlap has a size of 1,548 bp. The anti-hsp83 ORF does not show significant homology to any known gene sequences. In addition, no similar LAC ORF structures were found
in homologous gene regions of other organisms.
Received: 18 April 1997 / Accepted: 1 August 1997 相似文献
4.
In the course of investigating mitochondrial genome organization in Crypthecodinium cohnii, a non-photosynthetic dinoflagellate, we identified four EcoRI fragments that hybridize to a probe specific for cox1, the gene that encodes subunit 1 of cytochrome oxidase. Cloning and sequence characterization of the four fragments (5.7,
5.1, 4.1, 3.5 kilobase pairs) revealed that cox1 exists in four distinct but related contexts in C. cohnii mtDNA, with a central repeat unit flanked by one of two possible upstream (flanking domain 1 or 2) and downstream (flanking
domain 3 or 4) regions. The majority of the cox1 gene is located within the central repeat; however, the C-terminal portion of the open reading frame extends into flanking
domains 3 and 4, thereby creating two distinct cox1 coding sequences. The 3′-terminal region of one of the cox1 reading frames can assume an elaborate secondary structure, which potentially could act to stabilize the mature mRNA against
nucleolytic degradation. In addition, a high density of small inverted repeats (15–22 base pairs) has been identified at the
5′-end of cox1, further suggesting that hairpin structures could be important for gene regulation. The organization of cox1 in C. cohnii mtDNA appears to reflect homologous recombination events within the central repeat between different cox1 sequence contexts. Such recombining repeats are a characteristic feature of plant (angiosperm) mtDNA, but they have not previously
been described in the mitochondrial genomes of protists.
Received: 21 December 2000 / Accepted: 30 January 2001 相似文献
5.
6.
This study explored whether Dictyostelium discoideum can be used to express the avian Na,K-ATPase, a heterodimeric membrane protein. Dictyostelium was able to express mRNAs encoding the avian Na,K-ATPase subunits. However, Dictyostelium expressed avian Na,K-ATPase protein when only when a Dictyostelium consensus ribosomal binding sequence, AAAATAAA, was inserted in front of the open reading frames of the α1- and β1-subunit cDNAs and the first eight codons following the start-translation codons were changed to Dictyostelium preferred codons. These modified mRNAs appeared to be much less stable than the forms that were not readily translated. Dictyostelium could express the avian β-subunit alone but only expressed the α1-subunit when the β1-subunit was co-expressed. Subunit assembly occurred in cells expressing both α1- and β1-subunits. The bulk of the exogenously expressed sodium pump subunits remained in an intracellular compartment, presumed to
be the endoplasmic reticulum. Dictyostelium exported little or no Na,K-ATPase or free β-subunit to the plasma membrane.
Received: 7 July 1998/Revised: 8 October 1998 相似文献
7.
Protein-tyrosine dephosphorylation is a major mechanism in cellular regulation. A large number of protein-tyrosine phosphatases
is known from Eukarya, and more recently bacterial homologues have also been identified. By employing conserved sequence patterns
from both eukaryotic and bacterial protein-tyrosine phosphatases, we have identified three homologous sequences in two of
the four complete archaeal genomes. Two hypothetical open reading frames in the genome of Methanococcus jannaschii (MJ0215 and MJECL20) and one in the genome of Pyrococcus horikoshii (PH1732) clearly bear all the conserved residues of this family. No homologues were found in the genomes of Archaeoglobus fulgidus and Methanobacterium thermoautotrophicum. This is the first report of protein-tyrosine phosphatase sequences in Archaea.
Received: 29 April 1998 / Accepted: 27 November 1998 相似文献
8.
Charles Robin Robyn J. Russell Kerrie M. Medveczky John G. Oakeshott 《Journal of molecular evolution》1996,43(3):241-252
The α-esterase cluster of D. melanogaster contains 11 esterase genes dispersed over 60 kb. Embedded in the cluster are two unrelated open reading frames that have
sequence similarity with genes encoding ubiquitin-conjugating enzyme and tropomyosin. The esterase amino acid sequences show
37–66% identity with one another and all but one have all the motifs characteristic of functional members of the carboxyl/cholinesterase
multigene family. The exception has several frameshift mutations and appears to be a pseudogene. Patterns of amino acid differences
among cluster members in relation to generic models of carboxyl/cholinesterase protein structure are broadly similar to those
among other carboxyl/cholinesterases sequenced to date. However the α-esterases differ from most other members of the family
in: their lack of a signal peptide; the lack of conservation in cysteines involved in disulfide bridges; and in four indels,
two of which occur in or adjacent to regions that align with proposed substrate-binding sites of other carboxyl/cholinesterases.
Phylogenetic analyses clearly identify three simple gene duplication events within the cluster. The most recent event involved
the pseudogene which is located in an intron of another esterase gene. However, relative rate tests suggest that the pseudogene
remained functional after the duplication event and has become inactive relatively recently. The distribution of indels also
suggests a deeper node in the gene phylogeny that separates six genes at the two ends of the cluster from a block of five
in the middle.
Received: 18 January 1996 / Accepted: 12 March 1996 相似文献
9.
10.
Southern hybridization data suggest that the male sex-determining locus, Sry, is often duplicated in rodents. Here we explore DNA sequence evolution of orthologous and paralogous copies of Sry isolated from six species of African murines. PCR amplification followed by direct sequencing revealed from two to four copies
of Sry per species. All copies include a long open reading frame, with a stop codon that coincides closely with the stop codon of
the house mouse, Mus musculus, a species known to have a single copy of Sry. A phylogenetic analysis suggests that there are at least seven paralogous copies of Sry in this group of rodents. Putative orthologues are identical; sequence divergence among putative paralogues ranges from 1
to 8% (excluding the CAG repeat), with much lower levels of divergence in the high-mobility group (HMG-box) region than in
the C-terminal region. A high proportion of nucleotide substitutions in both regions result in amino-acid replacement. The
long open reading frame, conserved HMG-box, and pattern of evolution of the putative paralogues suggest that they are functional.
Received: 4 October 1996 / Accepted: 17 January 1997 相似文献
11.
Potenza N del Gaudio R Rivieccio L Russo GM Geraci G 《Journal of molecular evolution》2002,54(3):312-321
A novel member of the innexin family (cv-inx) has been isolated from the annelid polychaete worm Chaetopterus variopedatus using a PCR approach on genomic DNA and sequence analysis on genomic DNA clones. The gene is present in a HindIII-HindIII segment of 2250 bp containing an uninterrupted open reading frame of 1196 bp encoding a protein of 399 amino acids. The
predicted protein shows the typical structural features of innexins and consensus sites for phosphorylation. Analyses on genomic
DNA demonstrate that cv-inx is a single copy gene with no introns in the coding region, exactly corresponding to the cDNA
sequence. The gene expression is regulated during development as shown by Northern blots analyses of the RNA and by immunoreaction
with antibodies against the protein at several embryonic stages. The finding of an innexin in the phylum Annelida, outside
of the Ecdysozoa clade, and its peculiar gene structure suggest the necessity to reconsider the current hypothesis on the
origin and evolution of gap junctional proteins.
Received: 15 December 2000 / Accepted: 27 August 2001 相似文献
12.
We describe here a repetitive chromosomal element, which appears to be an insertion sequence, isolated from Clavibacter xyli subsp. cynodontis, a gram-positive plant-associated bacterium. The element, IS1237, is 905 bp in size, is bounded by 19-bp perfect inverted repeats and 3-bp direct repeats, and appears at least 16 times in the genome. It contains three open reading frames which show similarity to open reading frames from various other insertion sequences. We have found that there are two groups of related mobile elements: one in which two open reading frames are read separately and the other in which these two open reading frames are fuse together to give one predicted protein product. Using one of these open reading frames to search amino acid sequence databases, we found two instances in which similar reading frames flank genes carried on plasmids. We believe therefore that these plasmid-borne genes may be parts of previously unidentified mobile elements. For IS1237, a frameshift in two of the open reading frames and a stop codon in the third may indicate that this particular copy of the element is no longer active in transposition. The similarity of IS1237 to other elements from both gram-negative and gram-positive bacteria provides further evidence that mobile elements have been transferred between these two bacterial groups. 相似文献
13.
Klaus Melchers Thomas Wiegert Anita Buhmann Stefan Postius Klaus P. Schäfer W. Schumann 《Archives of microbiology》1998,169(5):393-396
Cloning and sequencing of an approximately 6.0-kb chromosomal DNA fragment from Helicobacter felis revealed five complete open reading frames. The deduced amino acid sequence of one ORF exhibited sequence similarity to the
FtsH protein, an ATP-dependent metalloprotease, from various bacterial species. The encoded protein consists of 638 amino
acid residues with a molecular mass of 70.2 kDa. The hydropathy profile of the FtsH protein predicted two N-terminal transmembrane
regions that were confirmed experimentally. Insertion of ftsH into a new versatile expression vector resulted in overexpression of FtsH protein in Escherichia coli. In addition, the E. coli ftsH gene could be replaced by the H. felis homologue to allow reduced growth and tenfold increased lysogenization by temperate phage λ.
Received: 6 November 1997 / Accepted: 22 January 1998 相似文献
14.
One of the most remarkable biochemical differences between the members of two domains Archaea and Bacteria is the stereochemistry
of the glycerophosphate backbone of phospholipids, which are exclusively opposite. The enzyme responsible to the formation
of Archaea-specific glycerophosphate was found to be NAD(P)-linked sn-glycerol-1-phosphate (G-1-P) dehydrogenase and it was first purified from Methanobacterium thermoautotrophicum cells and its gene was cloned. This structure gene named egsA (enantiomeric glycerophosphate synthase) consisted of 1,041 bp and coded the enzyme with 347 amino acid residues. The amino
acid sequence deduced from the base sequence of the cloned gene (egsA) did not share any sequence similarity except for NAD-binding region with that of NAD(P)-linked sn-glycerol-3-phosphate (G-3-P) dehydrogenase of Escherichia coli which catalyzes the formation of G-3-P backbone of bacterial phospholipids, while the deduced protein sequence of the enzyme
revealed some similarity with bacterial glycerol dehydrogenases. Because G-1-P dehydrogenase and G-3-P dehydrogenase would
originate from different ancestor enzymes and it would be almost impossible to interchange stereospecificity of the enzymes,
it seems likely that the stereostructure of membrane phospholipids of a cell must be maintained from the time of birth of
the first cell. We propose here the hypothesis that Archaea and Bacteria were differentiated by the occurrence of cells enclosed
by membranes of phospholipids with G-1-P and G-3-P as a backbone, respectively.
Received: 24 March 1997 / Accepted: 21 May 1997 相似文献
15.
Christiane Elie Marie- France Baucher Christian Fondrat Patrick Forterre 《Journal of molecular evolution》1997,45(1):107-114
We have isolated a new gene encoding a putative 103-kDa protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Analysis of the deduced amino-acid sequence shows an extended central domain, predicted to form coiled-coil structures, and
two terminal domains that display purine NTPase motifs. These features are reminiscent of mechanochemical motor proteins which
use the energy of ATP hydrolysis to move specific cellular components. Comparative analysis of the amino-acid sequence of
the terminal domains and predicted structural organization of this putative purine NTPase show that it is related both to
eucaryal proteins from the ``SMC family' involved in the condensation of chromosomes and to several bacterial and eucaryal
proteins involved in DNA recombination/repair. Further analyses revealed that these proteins are all members of the so called
``UvrA-related NTP-binding proteins superfamily' and form a large subgroup of motor-like NTPases involved in different DNA
processing mechanisms. The presence of such protein in Archaea, Bacteria, and Eucarya suggests an early origin of DNA-motor
proteins that could have emerged and diversified by domain shuffling.
Received: 29 June 1996 / Accepted: 28 February 1997 相似文献
16.
P. J. Keeling H.-P. Klenk Rama K. Singh Margret E. Schenk Christoph W. Sensen Wolfram Zillig W. Ford Doolittle 《Extremophiles : life under extreme conditions》1998,2(4):391-393
The complete sequence of the plasmid pRN2 from the thermoacidophile Sulfolobus islandicus has been determined. The plasmid was found to be circular and 6959 bp in length. S. islandicus harbors another endogenous plasmid, pRN1, and comparison of pRN1 and pRN2 revealed that these two plasmids are essentially
homologous, although very distantly related. pRN1 and pRN2 share several stretches of highly conserved noncoding DNA and three
common open reading frames. Two of these reading frames are likely related to replication, one encoding a large protein with
a helicase domain similar to viral helicases, and the other a copy number control protein, CopG.
Received: November 19, 1997 / Accepted: March 10, 1998 相似文献
17.
We have isolated a 29,000-Da carbonic anhydrase (CA) protein from the zebrafish, Danio rerio, sequenced two peptide fragments, and tentatively identified it as a high-activity CA by inhibition kinetics. We have also
characterized a 1,537-bp message whose deduced sequence of 260 amino acids matches that of the isolated protein. This CA is
clearly an α-CA based on the similarity of its sequence to that of other members of the α-CA gene family. A phylogenetic analysis
suggested CAH-Z diverged after the branching of the CA-V and CA-VII genes and prior to the duplications that generated the
CA-I, CA-II, and CA-III genes of amniotes. This marks the first characterization of the mRNA and its protein product from
the CA gene of a teleost.
Received: 31 March 1996 / Accepted: 8 September 1996 相似文献
18.
Alessandra Bonci Alessandra Chiesurin Patrizia Muscas Gian Maria Rossolini 《Journal of molecular evolution》1997,44(3):299-309
The structure of a Salmonella enterica serovar typhi gene located within the fim gene cluster and encoding a putative periplasmic chaperone-like protein involved in the assembly of type 1 pili was determined.
This gene, named fimC, has the ability to encode a 26-kDa polypeptide which is similar, at the sequence level, to the PapD periplasmic chaperonin
mediating the assembly of P pili of Escherichia coli, as well as to other periplasmic chaperone-like proteins involved in the biogenesis of pili or capsule-like structures of
various Gram-negative bacteria. A comprehensive search through the literature and sequence databases identified 31 (putative)
bacterial proteins that can be included in this protein family on the basis of sequence similarity. Results of a multiple
sequence comparison analysis showed that several residues, including most of those known to be critical in maintaining the
three-dimensional structure of PapD, are either conserved or conservatively substituted in all these proteins, suggesting
an overall similar folding for all of them. It was also evident that members of this family are clustered into different subfamilies
according to structural and phyletic data.
Received: 15 February 1996 / Accepted: 3 October 1996 相似文献
19.
Liu Hongtu; Haga Koki; Kasahara Yasuhiro; Ogasawara Naotake; Takahashi Hideo; Yoshikawa Hirofumi 《DNA research》1997,4(5):325-328
As a part of the Bacillus subtilis genome sequencing project,we have determined a 25-kb sequence covering the 17°19°region. This region contains 26 complete open reading frames(ORFs) including the alkA and adaA/B operon, which encode genesfor adaptive response to DNA alkylation. A homology search forthe newly identified 21 ORFs revealed that 4 of them exhibita significant similarity to known proteins, e.g., methicillin-resistantStaphylococcus aureus (MRSA) protein homolog, proteins involvedin chloramphenicol resistance, glucosamine synthase and an ABCtransporter protein. The remaining 17 ORFs did not show anysignificant sequence similarities to known gene products inthe database. 相似文献
20.
Ana I. Antón Antonio J. Martínez-Murcia Francisco Rodríguez-Valera 《Journal of molecular evolution》1998,47(1):62-72
The ribosomal RNA multigene family in Escherichia coli comprises seven rrn operons of similar, but not identical, sequence. Four operons (rrnC, B, G, and E) contain genes in the 16S–23S intergenic spacer region (ISR) for tRNAGlu-2 and three (rrnA, D, and H) contain genes for tRNAIle-1 and tRNAAla-1B. To increase our understanding of their molecular evolution, we have determined the ISR sequence of the seven operons in
a set of 12 strains from the ECOR collection. Each operon was specifically amplified using polymerase chain reaction primers
designed from genes or open reading frames located upstream of the 16S rRNA genes in E. coli K12. With a single exception (ECOR 40), ISRs containing one or two tRNA genes were found at the same respective loci as those
of strain K12. Intercistronic heterogeneity already found in K12 was representative of most variation among the strains studied
and the location of polymorphic sites was the same. Dispersed nucleotide substitutions were very few but 21 variable sites
were found grouped in a stem-loop, although the secondary structure was conserved. Some regions were found in which a stretch
of nucleotides was substituted in block by one alternative, apparently unrelated, sequence (as illustrated by the known putative
insertion of rsl in K12). Except for substitutions of different sizes and insertions/deletions found in the ISR, the pattern of nucleotide
variation is very similar to that found for the 16S rRNA gene in E. coli. Strains K12 and ECOR 40 showed the highest intercistronic heterogeneity. Most strains showed a strong tendency to homogenization.
Concerted evolution could explain the notorious conservation of this region that is supposed to have low functional restrictions.
Received: 31 July 1997 / Accepted: 17 October 1997 相似文献