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Expression of many bacterial genes is regulated by formation of alternative secondary RNA structure within the leader mRNA sequence. Our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and gamma-proteobacteria. The attenuators of these operons are predicted for genomes of some poorly known gamma-proteobacteria including Shewanella putrefaciens, attenuators of the tryptophan operon in some alpha-proteobacteria are also predicted. 相似文献
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Gunnar Von Heune 《Journal of theoretical biology》1982,97(2):227-238
The attenuator control mechanism, used in a number of amino acid biosynthetic operons, is considered from a theoretical point of view. The physics of RNA hairpin-loop formation is discussed, and rules for predicting which codons in the leader peptide that will affect operon expression are suggested. Manabe's (1981) stochastic model for the attenuator mechanism is used to analyse a number of known attenuators, showing a need for a “polymerase pause-site” in most of the attenuators, and providing some quantitative arguments in favour of the use of unusual codons in the control region. 相似文献
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Homma K Fukuchi S Nakamura Y Gojobori T Nishikawa K 《Molecular biology and evolution》2007,24(3):805-813
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The evolutionary stability of attenuators that mask information about animals that social partners can exploit 下载免费PDF全文
Signals and cues are fundamental to social interactions. A well‐established concept in the study of animal communication is an amplifier, defined as a trait that does not add extra information to that already present in the original cue or signal, but rather enhances the fidelity with which variation in the original cue or signal is correctly perceived. Attenuators as the logical compliment of amplifiers: attenuators act to reduce the fidelity with which variation in a signal or cue can be reliably evaluated by the perceivers. Where amplifiers reduce the effect of noise on the perception of variation, attenuators add noise. Attenuators have been subject to much less consideration than amplifiers; however, they will be the focus of our theoretical study. We utilize an extension of a well‐established model incorporated signal or cue inaccuracy and costly investments by emitter and perceiver in sending and attending to the signal or cue. We present broad conditions involving some conflict of interest between emitter and perceiver where it may be advantageous for emitters to invest in costly attenuators to mask cues from potential perceivers, and a subset of these conditions where the perceiver may be willing to invest in costly anti‐attenuators to mitigate the loss of information to them. We demonstrate that attenuators can be evolutionary stable even if they are costly, even if they are sometimes disadvantageous and even if a perceiver can mount counter‐measures to them. As such, we feel that attenuators of cues may be deserving of much more research attention. 相似文献
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The organization of ribosomal proteins in 16 prokaryotic genomes was studied as an example of comparative genome analyses of gene systems. Hypothetical ribosomal protein-containing operons were constructed. These operons also contained putative genes and other non-ribosomal genes. The correspondences among these genes across different organisms were clarified by sequence homology computations. In this way a cross tabulation of 70 ribosomal proteins genes was constructed. On average, these were organized into 9-14 operons in each genome. There were also 25 non-ribosomal or putative genes in these mainly ribosomal protein operons. Hence the table contains 95 genes in total. It was found that: (i) the conservation of the block of about 20 r-proteins in the L3 and L4 operons across almost the entire eubacteria and ar-chaebacteria is remarkable; (ii) some operons only belong to eubacteria or archaebacte-ria; (iii) although the ribosomal protein operons are highly conserved within domain, there are fine variat 相似文献
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The organization of ribosomal proteins in 16 prokaryotic genomes was studied as an example of comparative genome analyses of gene systems. Hypothetical ribosomal protein-containing operons were constructed. These operons also contained putative genes and other non-ribosomal genes. The correspondences among these genes across different organisms were clarified by sequence homology computations. In this way a cross tabulation of 70 ribosomal proteins genes was constructed. On average, these were organized into 9-14 operons in each genome. There were also 25 non-ribosomal or putative genes in these mainly ribosomal protein operons. Hence the table contains 95 genes in total. It was found that: (i) the conservation of the block of about 20 r-proteins in the L3 and L4 operons across almost the entire eubacteria and archaebacteria is remarkable; (ii) some operons only belong to eubacteria or archaebacteria; (iii) although the ribosomal protein operons are highly conserved within domain, there are fine variations in some operons across different organisms within each domain, and these variations are informative on the evolutionary relations among the organisms. This method provides a new potential for studying the origin and evolution of old species. 相似文献
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The Anabaena sensory rhodopsin transducer (ASRT) is a small protein that has been claimed to function as a signaling molecule downstream
of the cyanobacterial sensory rhodopsin. However, orthologs of ASRT have been detected in several bacteria that lack rhodopsin,
raising questions about the generality of this function. Using sequence profile searches we show that ASRT defines a novel
superfamily of β-sandwich fold domains. Through contextual inference based on domain architectures and predicted operons and
structural analysis we present strong evidence that these domains bind small molecules, most probably sugars. We propose that
the intracellular versions like ASRT probably participate as sensors that regulate a diverse range of sugar metabolism operons
or even the light sensory behavior in Anabaena by binding sugars or related metabolites. We also show that one of the extracellular versions define a predicted sugar-binding
structure in a novel cell-surface lipoprotein found across actinobacteria, including several pathogens such as Tropheryma, Actinomyces and Thermobifida. The analysis of this superfamily also provides new data to investigate the evolution of carbohydrate binding modes in β-sandwich
domains with very different topologies. 相似文献
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L. Otten P. De Ruffray P. de Lajudie B. Michot 《Molecular & general genetics : MGG》1996,251(1):99-107
One of the four ribosomal RNA operons (rrnA) from theAgrobacterium vitis vitopine strain S4 was sequenced.rrnA is most closely related to therrn operons ofBradyrhizobium japonicum andRhodobacter sphaeroides and carries an fMet-tRNA gene downstream of its 5S gene, as in the case ofR. sphaeroides. The 16S rRNA sequence of S4 differs from theA. vitis K309 type strain sequence by only one nucleotide, in spite of the fact that S4 and K309 have very different Ti plasmids. The predicted secondary structure of the S4 23S rRNA shows several features that are specific for the alpha proteobacteria, and an unusual branched structure in the universal B8 stem. The 3 ends of the three otherrrn copies of S4 were also cloned and sequenced. Sequence comparison delimits the 3 ends of the four repeats and defines two groups:rrnA/rrnB andrrnC/rrnD. 相似文献
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Steven G. Sedgwick David Lodwick Noel Doyle Helen Crowne Peter Strike 《Molecular & general genetics : MGG》1991,229(3):428-436
Summary The umuDC operons of Escherichia coli and Salmonella typhimurium and the analogous plasmid operons mucAB and impCAB have been previously characterized in terms of their roles in DNA repair and induced mutagenesis by radiation and many chemicals. The interrelationships of these mutagenic DNA repair operons were examined in vivo in functional tests of interchangeability of operon subunits in conferring UV resistance and UV mutability phenotypes to wild-type S. typhimurium and umu mutants of E. coli. This approach was combined with DNA and protein sequence comparisons between the four operons and a fifth operon, samAB, from the S. typhimurium LT2 cryptic plasmid. Components of the E. coli and S. typhimurium umu operons were reciprocally interchangeable whereas impCA and mucA could not function with umuC in either of these species. mucA and impB could also combine to give a mutagenic response to UV. These active combinations were associated with higher degrees of conservation of protein sequence than in other heterologous gene combinations and related to specific regions of sequence that may specify subunit interactions. The dominance of the E. coli umuD44 mutation over umuD was revealed in both wild-type E. coli and S. typhimurium and also demonstrated against impCAB. Finally interspecies transfer showed that the apparently poor activity of the S. typhimurium umuD gene in situ is not the result of an inherent defect in umuD but is due to the simultaneous presence of the S. typhimurium umuC sequence. It is suggested that the limitation of umuD activity by umuC in S. typhimurium is the basis of the poor induced mutability of this organism. 相似文献
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A DNA sequence containing the control sites for gene malT and for the malPQ operon 总被引:14,自引:0,他引:14
Summary The order of 802 base pairs was established in a DNA segment containing the promoter for malPQ which is one of the three maltose operons, and the promoter for malT, the positive regulator gene of the maltose regulon. The determination of the amino-terminal sequence of the MalT protein allowed us to identify the beginning of the malT gene on the sequence. The position of the malP gene was deduced from the published amino-terminal sequence of maltodextrin phosphorylase. A total of 611 base pairs separate the initiation codons for these two genes, which are transcribed in opposite directions. This large intergenic region does not code for any polypeptide of significant size. The main features of this sequence are discussed in terms of the regulation known to operate on malT and malPQ expression. 相似文献
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Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level 总被引:25,自引:0,他引:25
We have analyzed what phylogenetic signal can be derived by small subunit
rRNA comparison for bacteria of different but closely related genera
(enterobacteria) and for different species or strains within a single genus
(Escherichia or Salmonella), and finally how similar are the ribosomal
operons within a single organism (Escherichia coli). These sequences have
been analyzed by neighbor-joining, maximum likelihood, and parsimony. The
robustness of each topology was assessed by bootstrap. Sequences were
obtained for the seven rrn operons of E. coli strain PK3. These data
demonstrated differences located in three highly variable domains. Their
nature and localization suggest that since the divergence of E. coli and
Salmonella typhimurium, most point mutations that occurred within each gene
have been propagated among the gene family by conversions involving short
domains, and that homogenization by conversions may not have affected the
entire sequence of each gene. We show that the differences that exist
between the different operons are ignored when sequences are obtained
either after cloning of a single operon or directly from polymerase chain
reaction (PCR) products. Direct sequencing of PCR products produces a mean
sequence in which mutations present in the most variable domains become
hidden. Cloning a single operon results in a sequence that differs from
that of the other operons and of the mean sequence by several point
mutations. For identification of unknown bacteria at the species level or
below, a mean sequence or the sequence of a single nonidentified operon
should therefore be avoided. Taking into account the seven operons and
therefore mutations that accumulate in the most variable domains would
perhaps increase tree resolution. However, if gene conversions that
homogenize the rRNA multigene family are rare events, some nodes in
phylogenetic trees will reflect these recombination events and these trees
may therefore be gene trees rather than organismal trees.
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Valley Stewart 《Molecular microbiology》1993,9(3):425-434
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Josefa Bezerra da Silva Eneas Carvalho Rudy A. Hartskeerl Paulo L. Ho 《Current microbiology》2011,62(2):525-524
Leptospirosis is an important epidemic zoonosis worldwide. Currently, there are more than 250 Leptospira pathogenic serovars known that can potentially infect humans. Conventional classification of leptospires with the serovar
as the basic taxon, based on serological recognition of lipopolysaccharide (LPS) composition does not correlate well with
species determination, based on general genomic features. Here, we investigate the selective amplification of polymorphic
regions from the LPS biosynthesis loci (rfb) as a potential tool for serovar typing of Leptospira interrogans species. Eight pairs of primers were designed to target six ORFs from the rfb operon with varying levels of sequence polymorphism. They were tested both separately and multiplexed. Half of these primer
pairs produced serovar-specific amplicons, allowing the identification of some specific serovars and also groups of serovars.
It was shown that the serovar classification of Leptospira can be accessed by selective amplification of rfb operons in some cases, which may permit a parallel between the serological and the genomic classifications of Leptospira. As a conclusion, the selective amplification of rfb generated promising and already useful results, but it appears necessary to characterize a larger variety of Leptospira genomes or rfb operons to fully develop this method. 相似文献