| sequence analysis of an aphid endosymbiont dna fragment containing rpob (beta-subunit of rna polymerase) and portions of rpll and rpoc. | the aphid schizaphis graminum is dependent on an association with a prokaryotic endosymbiont (buchnera aphidicola). the nucleotide (nt) sequence of a 5040 base pair (bp) dna fragment of b. aphidicola, homologous to the rpll-rpob-rpoc portion of the escherichia coli beta operon, was determined. the dna coded for the terminal 35 amino acids of rpll (large ribosomal subunit protein l7/l12), the complete rpob (beta-subunit of rna polymerase), and the first 209 amino acids of rpoc (beta'-subunit of r ... | 1992 | 1369199 |
| sequence analysis of a dna fragment from buchnera aphidicola (an endosymbiont of aphids) containing genes homologous to dnag, rpod, cyse, and secb. | the aphid, schizaphis graminum, contains a prokaryotic, obligately intracellular endosymbiont, buchnera aphidicola, which is necessary for the survival of the host. a recent study of bu. aphidicola 16s rrna has indicated that it is a member of the gamma-3 subdivision of the eubacterial class, proteobacteria, which includes escherichia coli. in order to further characterize the endosymbiont and establish its similarity to free-living eubacteria and/or organelles, we have cloned and sequenced a 45 ... | 1992 | 1398077 |
| genetic analysis of an aphid endosymbiont dna fragment homologous to the rnpa-rpmh-dnaa-dnan-gyrb region of eubacteria. | buchnera aphidicola is a gram- eubacterium with a dna g+c content of 28-30 mol%. this organism is an obligate intracellular symbiont of aphids. to determine its similarity to or difference from other eubacteria, a 4.9-kb dna fragment from b. aphidicola containing the gene homologous to escherichia coli dnaa (a gene involved in the initiation of chromosome replication) was cloned into e. coli and sequenced. the order of genes on this fragment, 60k-10k-rnpa-rpmh-dnaa-dnan-gyrb, was similar to that ... | 1992 | 1572539 |
| buchnera aphidicola (a prokaryotic endosymbiont of aphids) contains a putative 16s rrna operon unlinked to the 23s rrna-encoding gene: sequence determination, and promoter and terminator analysis. | the aphid schizaphis graminum is dependent on an association with buchnera aphidicola, an eubacterial endosymbiont located in specialized host cells. past studies have indicated that escherichia coli is the closest known relative of the endosymbiont which has many genetic attributes of free-living bacteria. in order to obtain information on the properties of highly expressed genes, we have chosen for study the single-copy rrs (gene encoding 16s rrna) of b. aphidicola. a 4.4-kb dna fragment was c ... | 1993 | 7507875 |
| characterization of a putative 23s-5s rrna operon of buchnera aphidicola (endosymbiont of aphids) unlinked to the 16s rrna-encoding gene. | buchnera aphidicola (ba) is an endosymbiont of the aphid schizaphis graminum. in order to obtain information on highly expressed genes, we have chosen to study ba genes coding for rrnas. previously, the single-copy rrs gene was cloned and sequenced [munson et al., gene 137 (1993) 171-178], and found to constitute a single transcription unit unlinked to rrl and rrf. in the present study, a 6.1-kb ba dna fragment containing rrl was cloned into escherichia coli (ec) and sequenced. based on sequence ... | 1995 | 7535281 |
| molecular analysis of the endosymbionts of tsetse flies: 16s rdna locus and over-expression of a chaperonin. | based on 16s rdna sequence comparison, intracellular mycetome-associated endosymbionts (p-endosymbionts) of tsetse flies (diptera: glossinidae) form a distinct lineage within the gamma-3 subdivision of proteobacteria, related to the free-living bacterium escherichia coli, midgut s-endosymbionts of various insects including tsetse flies, and to the p-endosymbiont lineage of aphids, buchnera aphidicola. gene organization and expression of several loci in intracellular microorganisms have revealed ... | 1995 | 7538012 |
| wigglesworthia gen. nov. and wigglesworthia glossinidia sp. nov., taxa consisting of the mycetocyte-associated, primary endosymbionts of tsetse flies. | the primary endosymbionts (p-endosymbionts) of tsetse flies (diptera: glossinidae) are harbored inside specialized cells (mycetocytes) in the anterior region of the gut, and these specialized cells form a white, u-shaped organelle called mycetome. the p-endosymbionts of five tsetse fly species belonging to the glossinidae have been characterized morphologically, and their 16s ribosomal dna sequences have been determined for phylogenetic analysis. these organisms were found to belong to a distinc ... | 1995 | 7547309 |
| aspects of energy-yielding metabolism in the aphid, schizaphis graminum, and its endosymbiont: detection of gene fragments potentially coding for the atp synthase beta-subunit and glyceraldehyde-3-phosphate dehydrogenase. | specialized cells within the aphid, schizaphis graminum, contain intracellular, vesicle-enclosed eubacterial endosymbionts (buchnera aphidicola). using oligonucleotide probes derived from conserved sequences of the atp synthase beta-subunit and glyceraldehyde-3-phosphate dehydrogenase, and the polymerase chain reaction (pcr), we have amplified, cloned, and sequenced three dna fragments. amino acid sequence similarity indicated that two of these fragments corresponded to endosymbiont and host gen ... | 1993 | 7763501 |
| buchnera aphidicola (aphid-endosymbiont) glyceraldehyde-3-phosphate dehydrogenase: molecular cloning and sequence analysis. | buchnera aphidicola is an endosymbiont of the aphid schizaphis graminum. a 3.9-kb b. aphidicola dna fragment was sequenced and found to contain two open reading frames (orfs). the deduced amino acid sequence of one of the orfs had an 85% identity to escherichia coli glyceraldehyde-3-phosphate dehydrogenase (gap). both of these proteins have a higher similarity to eukaryotic than to prokaryotic gaps. the second orf could not be readily identified. the sequence of the putative product indicated th ... | 1995 | 7765846 |
| aromatic amino acid biosynthesis in buchnera aphidicola (endosymbiont of aphids): cloning and sequencing of a dna fragment containing aroh-thrs-infc-rpmi-rplt. | a 4.5-kilobase dna fragment from buchnera aphidicola, the endosymbiont of the aphid schizaphis graminum, was cloned and sequenced. on the basis of homology to escherichia coli, the following genes were found in the order listed: aroh-thrs-infc-rpmi-rplt. aroh corresponds to the e. coli tryptophan-inhibited 3-deoxy-d-arabino-heptulosonate-7-phosphate (dahp) synthase. evidence was presented indicating that this is the sole gene for dahp synthase in the b. aphidicola genome. this enzyme initiates t ... | 1995 | 7766160 |
| amplification of trpeg: adaptation of buchnera aphidicola to an endosymbiotic association with aphids. | survival of aphids is dependent on an association with a prokaryotic endosymbiont (buchnera aphidicola) found in specialized cells within the aphid body cavity. recent nutritional and physiological studies have indicated that one of the functions of the endosymbionts is the synthesis of tryptophan [douglas, a. e. & prosser, w. a. (1992) j. insect physiol. 38, 565-568]. b. aphidicola resembles in many of its properties free-living prokaryotes. an adaptation to an endosymbiosis involving the overp ... | 1994 | 8170994 |
| molecular cloning and nucleotide sequence of a putative trpdc(f)ba operon in buchnera aphidicola (endosymbiont of the aphid schizaphis graminum). | a 8,392-nucleotide-long dna fragment from buchnera aphidicola (endosymbiont of the aphid schizaphis graminum) contained five genes of the tryptophan biosynthetic pathway [trpdc(f)ba] which code for enzymes converting anthranilate to tryptophan. these genes are probably arranged as a single transcription unit. downstream of the trp genes were orf-v, orf-vi, and p14, three open reading frames which in escherichia coli are also found downstream of the trp operon. upstream of the b. aphidicola trp g ... | 1993 | 8407819 |
| ribosomal protein s1 (rpsa) of buchnera aphidicola, the endosymbiont of aphids: characterization of the gene and detection of the product. | buchnera aphidicola is a prokaryotic endosymbiont found in specialized cells of the aphid schizaphis graminum. many of the previously cloned b. aphidicola genes are preceded by a poor ribosome-binding site. ribosomal protein s1 (rpsa) allows the translation of messenger rnas that lack or have a poor ribosome binding site. we have cloned and sequenced a 4.5-kilobase (kb) b. aphidicola dna fragment containing four open reading frames corresponding to aroa-rpsa-himd-tpia. the deduced amino acid seq ... | 1996 | 8574133 |
| molecular characterization of cyclic and obligate parthenogens in the aphid rhopalosiphum padi (l.). | holocyclic clones of the aphid rhopalosiphum padi (l.) reproduce by cyclic parthenogenesis, whereas anholocyclic individuals are obligate parthenogens. mitochondrial dna and (mtdna) and random amplified polymorphic dna markers in r. padi as well as plasmid dna markers of its bacterial endosymbiont, buchnera aphidicola, were examined to determine the extent of genetic divergence between clones with these differing breeding systems. these analyses revealed that cyclically parthenogenetic lineages ... | 1996 | 8637928 |
| evolution of dnaq, the gene encoding the editing 3' to 5' exonuclease subunit of dna polymerase iii holoenzyme in gram-negative bacteria. | the nucleotide sequences of the dnaq genes from salmonella typhimurium and buchnera aphidicola, encoding the epsilon-subunit of the dna polymerase iii holoenzyme, have been determined. the salmonella typhimurium dnaq protein consists of 243 amino acid residues with a calculated molecular weight of 27224. the buchnera aphidicola dnaq protein contains 233 amino acid residues with a calculated molecular weight of 27170. a multiple sequence alignment of the amino acid sequences of the dnaq proteins ... | 1997 | 9000520 |
| protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase. | evolutionary analysis indicates that eubacterial nadp-dependent isocitrate dehydrogenases (ec 1.1.1.42) first evolved from an nad-dependent precursor about 3.5 billion years ago. selection in favor of utilizing nadp was probably a result of niche expansion during growth on acetate, where isocitrate dehydrogenase provides 90% of the nadph necessary for biosynthesis. amino acids responsible for differing coenzyme specificities were identified from x-ray crystallographic structures of escherichia c ... | 1997 | 9096353 |
| structure of the dnaa region of the endosymbiont, buchnera aphidicola, of aphid schizaphis graminum. | buchnera aphidicola is an intracellular prokaryote (endosymbiont) that lives in the body cavity of the aphid. phylogenetic studies indicated that it is closely related to escherichia coli and members of enterobacteria. the gene order of the region containing the dnaa gene is well conserved in many bacteria. seven genes of the endosymbiont of the aphid schizaphis graminum, gyrb, dnan, dnaa, rpmh, rnpa, yidd, and 60k. were found to be homologous in sequence and relative location to those of e. col ... | 1996 | 9097044 |
| the (f1f0) atp synthase of buchnera aphidicola (endosymbiont of aphids): genetic analysis of the putative atp operon. | buchnera aphidicola is an intracellular, non-cultivable prokaryotic symbiont of the aphid schizaphis graminum. a 6.8-kilobase fragment from b. aphidicola was cloned and sequenced and was found to contain genes encoding for proteins of the atp synthase. the order of the genes, atpbefhagdc, is identical to that found inescherichia coli and many other prokaryotes. this genetic organization is different from that observed in organelles such as mitochondria and chloroplasts, in which the genes are pa ... | 1997 | 9216881 |
| buchnera aphidicola (endosymbiont of aphids) contains nuoc(d) genes that encode subunits of nadh dehydrogenase. | a two-kilobase dna fragment from buchnera aphidicola, the endosymbiont of aphids, was cloned and sequenced. one open reading frame was detected, coding for a putative protein of 600 amino acids. the n-terminal portion of this protein corresponded to nuoc, while the c-terminal portion corresponded to nuod. these proteins are constituents of the membrane-associated nadh dehydrogenase. our results suggest that these two proteins are fused in buchnera aphidicola, a result consistent with their previ ... | 1997 | 9216887 |
| putative evolutionary origin of plasmids carrying the genes involved in leucine biosynthesis in buchnera aphidicola (endosymbiont of aphids). | an 8.5-kb plasmid encoding genes (leuabcd) involved in leucine biosynthesis and a small plasmid of 1.74 kb of yet unknown function were found in the intracellular symbiont, buchnera aphidicola, of two divergent aphid species, thelaxes suberi and tetraneura caerulescens, respectively. the leuabcd-carrying plasmid (pbts1) was amplified from total aphid dna by inverse long pcr, using outwardly oriented oligonucleotide primers specific to leua. the resulting 8.2-kb pcr fragment as well as the 1.74-k ... | 1997 | 9244264 |
| wolbachia run amok. | | 1997 | 9326576 |
| potato leafroll virus binds to the equatorial domain of the aphid endosymbiotic groel homolog. | a groel homolog with a molecular mass of 60 kda, produced by the primary endosymbiotic bacterium (a buchnera sp.) of myzus persicae and released into the hemolymph, has previously been shown to be a key protein in the transmission of potato leafroll virus (plrv). like other luteoviruses and pea enation mosaic virus, plrv readily binds to extracellular buchnera groel, and in vivo interference in this interaction coincides with reduced capsid integrity and loss of infectivity. to gain more knowled ... | 1998 | 9420234 |
| substrate ambiguity of 3-deoxy-d-manno-octulosonate 8-phosphate synthase from neisseria gonorrhoeae in the context of its membership in a protein family containing a subset of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthases. | 3-deoxy-d-manno-octulosonate 8-phosphate (kdop) synthase and 3-deoxy-d-arabino-heptulosonate 7-phosphate (dahp) synthase catalyze similar phosphoenolpyruvate-utilizing reactions. the genome of neisseria gonorrhoeae contains one gene encoding kdop synthase and one gene encoding dahp synthase. of the two nonhomologous dahp synthase families known, the n. gonorrhoeae protein belongs to the family i assemblage. kdop synthase exhibited an ability to replace arabinose-5-p with either erythrose-4-p or ... | 1998 | 9422601 |
| characterization of ftsz, the cell division gene of buchnera aphidicola (endosymbiont of aphids) and detection of the product. | buchnera aphidicola, the endosymbiont of the aphid schizaphis graminum, contains the gene ftsz, which codes for a protein involved in the initiation of septum formation during cell division. with immunological techniques, this protein has been detected in cell-free extracts of the endosymbiont. nucleotide sequence determination of a 6.4-kilobase b. aphidicola dna fragment has indicated that, as in e. coli, ftsz is adjacent to genes coding for other cell division proteins as well as genes involve ... | 1998 | 9425245 |
| genetic analysis of the nuo locus, which encodes the proton-translocating nadh dehydrogenase in escherichia coli. | complex i (ec 1.6.99.3) of the bacterium escherichia coli is considered to be the minimal form of the type i nadh dehydrogenase, the first enzyme complex in the respiratory chain. because of its small size and relative simplicity, the e. coli enzyme has become a model used to identify and characterize the mechanism(s) by which cells regulate the synthesis and assembly of this large respiratory complex. to begin dissecting the processes by which e. coli cells regulate the expression of nuo and th ... | 1998 | 9495756 |
| sequence analysis of a 34.7-kb dna segment from the genome of buchnera aphidicola (endosymbiont of aphids) containing groel, dnaa, the atp operon, gida, and rho. | buchnera aphidicola is a prokaryotic endosymbiont of the aphid schizaphis graminum. from past and present nucleotide sequence analyses of the b. aphidicola genome, we have assembled a 34. 7-kilobase (kb) dna segment. this segment contains genes coding for 32 open reading frames (orfs), which corresponded to 89.9% of the dna. all of these orfs could be identified with homologous regions of the escherichia coli genome. the order of the genes with established functions was groels-trme-rnpa-rpmh-dna ... | 1998 | 9516544 |
| deleterious mutations destabilize ribosomal rna in endosymbiotic bacteria. | in populations that are small and asexual, mutations with slight negative effects on fitness will drift to fixation more often than in large or sexual populations in which they will be eliminated by selection. if such mutations occur in substantial numbers, the combined effects of long-term asexuality and small population size may result in substantial accumulation of mildly deleterious substitutions. prokaryotic endosymbionts of animals that are transmitted maternally for very long periods are ... | 1998 | 9539759 |
| regulatory conservation and divergence of sigma32 homologs from gram-negative bacteria: serratia marcescens, proteus mirabilis, pseudomonas aeruginosa, and agrobacterium tumefaciens. | the heat shock response in escherichia coli is mediated primarily by the rpoh gene, encoding sigma32, which is specifically required for transcription of heat shock genes. a number of sigma32 homologs have recently been cloned from gram-negative bacteria that belong to the gamma or alpha subdivisions of the proteobacteria. we report here some of the regulatory features of several such homologs (rpoh) expressed in e. coli as well as in respective cognate bacteria. when expressed in an e. coli del ... | 1998 | 9573192 |
| identification of the gene encoding the tryptophan synthase beta-subunit from chlamydomonas reinhardtii. | we report the isolation of a chlamydomonas reinhardtii cdna that encodes the beta-subunit of tryptophan synthase (tsb). this cdna was cloned by functional complementation of a trp-operon-deleted strain of escherichia coli. hybridization analysis indicated that the gene exists in a single copy. the predicted amino acid sequence showed the greatest identity to tsb polypeptides from other photosynthetic organisms. with the goal of identifying mutations in the gene encoding this enzyme, we isolated ... | 1998 | 9625698 |
| molecular characterization of the principal symbiotic bacteria of the weevil sitophilus oryzae: a peculiar g + c content of an endocytobiotic dna. | the principal intracellular symbiotic bacteria of the cereal weevil sitophilus oryzae were characterized using the sequence of the 16s rdna gene (rrs gene) and g + c content analysis. polymerase chain reaction amplification with universal eubacterial primers of the rrs gene showed a single expected sequence of 1,501 bp. comparison of this sequence with the available database sequences placed the intracellular bacteria of s. oryzae as members of the enterobacteriaceae family, closely related to t ... | 1998 | 9664696 |
| sequence analysis of a dna fragment from buchnera aphidicola (aphid endosymbiont) containing the genes dapd-htra-ilvi-ilvh-ftsl-ftsi-mure | buchnera aphidicola is a prokaryotic endosymbiont of the aphid schizaphis graminum. one of the endosymbiont's functions is the synthesis of branched-chain amino acids. a 9.7-kilobase b. aphidicola chromosomal dna fragment was cloned and sequenced and found to contain genes encoding acetohydroxy acid synthase (ilvih), the first enzyme of the parallel pathway of isoleucine and valine biosynthesis. previously we have detected ilvc and ilvd, encoding the two other enzymes of this pathway. in additio ... | 1998 | 9688822 |
| comparison of sample sequences of the salmonella typhi genome to the sequence of the complete escherichia coli k-12 genome. | raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. to demonstrate the utility of such a resource, 870 single-stranded m13 clones were sequenced from a shotgun library of the salmonella typhi ty2 genome. the sequence reads averaged over 400 bases and sampled the genome with an average spacing of once every 5,000 bases. a total of 339,243 bases of unique sequence was generated (approximately 7% representation). ... | 1998 | 9712782 |
| buchnera aphidicola (aphid endosymbiont) contains genes encoding enzymes of histidine biosynthesis. | buchnera aphidicola is an endosymbiont of aphids. one of its functions appears to be the synthesis of essential amino acids for the aphid host. a 12.8-kilobase b. aphidicola dna fragment has been cloned and sequenced. it contains genes encoding all of the enzymes required for the biosynthesis of the essential amino acid histidine. the order of the genes, hisgdcbhafi, is the same as that found in escherichia coli and is consistent with their constituting a single transcription unit. the dna fragm ... | 1998 | 9767718 |
| structure and evolution of the leucine plasmids carried by the endosymbiont (buchnera aphidicola) from aphids of the family aphididae. | in all examined species of the family aphididae, the bacterial endosymbiont buchnera aphidicola carries a plasmid encoding the genes leuabcd (involved in leucine biosynthesis) along with repa1, repa2 and orf1. the gene organisation of the leucine plasmids was conserved, except in buchnera isolated from pterocomma populeum, where orf1 was located in a different position. an inverted repeat (lir1) located between repa2 and leua is found in all of the buchnera leucine plasmids examined. the predict ... | 1998 | 9812361 |
| the hsc66-hsc20 chaperone system in escherichia coli: chaperone activity and interactions with the dnak-dnaj-grpe system. | hsc66, a stress-70 protein, and hsc20, a j-type accessory protein, comprise a newly described hsp70-type chaperone system in addition to dnak-dnaj-grpe in escherichia coli. because endogenous substrates for the hsc66-hsc20 system have not yet been identified, we investigated chaperone-like activities of hsc66 and hsc20 by their ability to suppress aggregation of denatured model substrate proteins, such as rhodanese, citrate synthase, and luciferase. hsc66 suppressed aggregation of rhodanese and ... | 1998 | 9852006 |
| detection of messenger rna transcribed from genes encoding enzymes of amino acid biosynthesis in buchnera aphidicola (endosymbiont of aphids). | the aphid schizaphis graminum is dependent on buchnera aphidicola, a prokaryotic endosymbiont. one of the functions of the endosymbiont is the synthesis of essential amino acids for the aphid host. previously we have found that b. aphidicola has many of the genes that encode enzymes of amino acid biosynthesis. using reverse transcriptase and the polymerase chain reaction, we have detected messenger rna corresponding to genes involved in the synthesis of tryptophan, isoleucine, valine, leucine, a ... | 1999 | 9871114 |
| plasmid-encoded anthranilate synthase (trpeg) in buchnera aphidicola from aphids of the family pemphigidae. | buchnera aphidicola is an obligate intracellular symbiont of aphids. one of its proposed functions is the synthesis of essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. the genetic organization of the tryptophan pathway in buchnera from proliferous aphids of the family aphididae has previously been shown to reflect a capacity to overproduce this essential amino acid (c.-y. lai, l. baumann, and p. baumann, proc. natl. acad. sci. usa 91:3819-3823, ... | 1999 | 9872768 |
| rapid identification of thermotolerant campylobacter jejuni, campylobacter coli, campylobacter lari, and campylobacter upsaliensis from various geographic locations by a gtpase-based pcr-reverse hybridization assay. | recently, a gene from campylobacter jejuni encoding a putative gtpase was identified. based on two semiconserved gtp-binding sites encoded within this gene, pcr primers were selected that allow amplification of a 153-bp fragment from c. jejuni, c. coli, c. lari, and c. upsaliensis. sequence analysis of these pcr products revealed consistent interspecies variation, which allowed the definition of species-specific probes for each of the four thermotolerant campylobacter species. multiple probes we ... | 1999 | 10325325 |
| identification of a putative p-transporter operon in the genome of a burkholderia strain living inside the arbuscular mycorrhizal fungus gigaspora margarita. | this article reports the identification of a putative p-transporter operon in the genome of a burkholderia sp. living in the cytoplasm of the arbuscular mycorrhizal fungus gigaspora margarita. its presence suggests that burkholderia sp. has the potential for p uptake from this environment. this finding raises new questions concerning the importance of intracellular bacteria for mycorrhizal symbiosis. | 1999 | 10383982 |
| a chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes. | we provide data and analysis to support the hypothesis that the ancestor of animal mitochondria (mt) and many primitive amitochondrial (a-mt) eukaryotes was a fusion microbe composed of a clostridium-like eubacterium and a sulfolobus-like archaebacterium. the analysis is based on several observations: (i) the genome signatures (dinucleotide relative abundance values) of clostridium and sulfolobus are compatible (sufficiently similar) and each has significantly more similarity in genome signature ... | 1999 | 10430918 |
| characterization of mutations in the rpob gene in naturally rifampin-resistant rickettsia species. | rickettsiae are gram-negative, obligately intracellular bacteria responsible for arthropod-borne spotted fevers and typhus. experimental studies have delineated a cluster of naturally rifampin-resistant spotted fever group species. we sequenced the 4, 122- to 4,125-bp rna polymerase beta-subunit-encoding gene (rpob) from typhus and spotted fever group representatives and obtained partial sequences for all naturally rifampin-resistant species. a single point mutation resulting in a phenylalanine- ... | 1999 | 10508014 |
| cell division in escherichia coli: role of ftsl domains in septal localization, function, and oligomerization. | in escherichia coli, nine essential cell division proteins are known to localize to the division septum. ftsl is a 13-kda bitopic membrane protein with a short cytoplasmic n-terminal domain, a membrane-spanning segment, and a periplasmic domain that has a repeated heptad motif characteristic of leucine zippers. here, we identify the requirements for ftsl septal localization and function. we used green fluorescent protein fusions to ftsl proteins where domains of ftsl had been exchanged with anal ... | 2000 | 10613870 |
| molecular characterization of the leucine plasmid from buchnera aphidicola, primary endosymbiont of the aphid acyrthosiphon pisum. | the complete sequence of the leucine plasmid of buchnera aphidicola from the aphid acyrthosiphon pisum (pleu-bap) is reported. its gene organization was concordant with those of other leucine plasmids of buchnera from aphids of the aphidini and macrosiphini tribes. three inverted repeats are present in pleu-bap. two of them are also present in pleu from the family aphididae: (i) sir1, located downstream the leucine operon, resembles a rho-independent terminator of transcription, and (ii) lir1, l ... | 2000 | 10688696 |
| a missense mutation in the nuclear gene coding for the mitochondrial aspartyl-trna synthetase suppresses a mitochondrial trna(asp) mutation. | the nuclear suppressor allele nsm3 in strain ff1210-6c/170-e22 (e22), which suppresses a mutation of the yeast mitochondrial trna(asp)gene in saccharomyces cerevisiae, was cloned and identified. to isolate the nsm3 allele, a genomic dna library using the vector yep13 was constructed from strain e22. nine yep13 recombinant plasmids were isolated and shown to suppress the mutation in the mitochondrial trna(asp)gene. these nine plasmids carry a common 4. 5-kb chromosomal dna fragment which contains ... | 2000 | 10710420 |
| functional analysis of gapped microbial genomes: amino acid metabolism of thiobacillus ferrooxidans. | a gapped genome sequence of the biomining bacterium thiobacillus ferrooxidans strain atcc23270 was assembled from sheared dna fragments (3.2-times coverage) into 1,912 contigs. a total of 2,712 potential genes (orfs) were identified in 2.6 mbp (megabase pairs) of thiobacillus genomic sequence. of these genes, 2,159 could be assigned functions by using the wit-pro/emp genome analysis system, most with a high degree of certainty. nine hundred of the genes have been assigned roles in metabolic path ... | 2000 | 10737802 |
| prephenate dehydratase from the aphid endosymbiont (buchnera) displays changes in the regulatory domain that suggest its desensitization to inhibition by phenylalanine. | buchnera aphidicola, the prokaryotic endosymbiont of aphids, complements dietary deficiencies with the synthesis and provision of several essential amino acids. we have cloned and sequenced a region of the genome of b. aphidicola isolated from acyrthosiphon pisum which includes the two-domain aroq/phea gene. this gene encodes the bifunctional chorismate mutase-prephenate dehydratase protein, which plays a central role in l-phenylalanine biosynthesis. two changes involved in the overproduction of ... | 2000 | 10781569 |
| decoupling of genome size and sequence divergence in a symbiotic bacterium. | in contrast to genome size variation in most bacterial taxa, the small genome size of buchnera sp. was shown to be highly conserved across genetically diverse isolates (630 to 643 kb). this exceptional size conservation may reflect the inability of this obligate mutualist to acquire foreign dna and reduced selection for genetic novelty within a static intracellular environment. | 2000 | 10851009 |
| the secondary endosymbiotic bacterium of the pea aphid acyrthosiphon pisum (insecta: homoptera). | the secondary intracellular symbiotic bacterium (s-symbiont) of the pea aphid acyrthosiphon pisum was investigated to determine its prevalence among strains, its phylogenetic position, its localization in the host insect, its ultrastructure, and the cytology of the endosymbiotic system. a total of 14 aphid strains were examined, and the s-symbiont was detected in 4 japanese strains by diagnostic pcr. two types of eubacterial 16s ribosomal dna sequences were identified in disymbiotic strains; one ... | 2000 | 10877764 |
| cospeciation of psyllids and their primary prokaryotic endosymbionts. | psyllids are plant sap-feeding insects that harbor prokaryotic endosymbionts in specialized cells within the body cavity. four-kilobase dna fragments containing 16s and 23s ribosomal dna (rdna) were amplified from the primary (p) endosymbiont of 32 species of psyllids representing three psyllid families and eight subfamilies. in addition, 0.54-kb fragments of the psyllid nuclear gene wingless were also amplified from 26 species. phylogenetic trees derived from 16s-23s rdna and from the host wing ... | 2000 | 10877784 |
| the bacterial cell-division protein zipa and its interaction with an ftsz fragment revealed by x-ray crystallography. | in escherichia coli, ftsz, a homologue of eukaryotic tubulins, and zipa, a membrane-anchored protein that binds to ftsz, are two essential components of the septal ring structure that mediates cell division. recent data indicate that zipa is involved in the assembly of the ring by linking ftsz to the cytoplasmic membrane and that the zipa-ftsz interaction is mediated by their c-terminal domains. we present the x-ray crystal structures of the c-terminal ftsz-binding domain of zipa and a complex b ... | 2000 | 10880432 |
| accelerated evolution in bacterial endosymbionts of aphids. | when compared with free living bacteria, it is proposed that there are at least two endosymbiotic processes in aphids based on the a + t content as well as the increased evolutionary rate of the beta-subunit of the f-atpase complex in different endosymbiotic bacteria. the first well established process corresponds to the integration of buchnera aphidicola more than 150 million years ago. the other is postulated to correspond to new endosymbiotic processes in which the bacteria involved contain l ... | 1999 | 10943385 |
| postsymbiotic plasmid acquisition and evolution of the repa1-replicon in buchnera aphidicola. | buchnera aphidicola is an obligate, strictly vertically transmitted, bacterial symbiont of aphids. it supplies its host with essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. several lineages of buchnera show adaptation to their nutritional role in the form of plasmid-mediated amplification of key-genes involved in the biosynthesis of tryptophan (trpeg) and leucine (leuabcd). phylogenetic analyses of these plasmid-encoded functions have thus far ... | 2000 | 10984505 |
| vertical transmission of biosynthetic plasmids in aphid endosymbionts (buchnera). | this study tested for horizontal transfer of plasmids among buchnera aphidicola strains associated with ecologically and phylogenetically related aphid hosts (uroleucon species). phylogenetic congruence of buchnera plasmid (trpeg and leuabc) and chromosomal (dnan and trpb) genes supports strictly vertical long-term transmission of plasmids, which persist due to their contributions to host nutrition rather than capacity for infectious transfer. synonymous divergences indicate elevated mutation on ... | 2001 | 11133977 |
| degenerative minimalism in the genome of a psyllid endosymbiont. | psyllids, like aphids, feed on plant phloem sap and are obligately associated with prokaryotic endosymbionts acquired through vertical transmission from an ancestral infection. we have sequenced 37 kb of dna of the genome of carsonella ruddii, the endosymbiont of psyllids, and found that it has a number of unusual properties revealing a more extreme case of degeneration than was previously reported from studies of eubacterial genomes, including that of the aphid endosymbiont buchnera aphidicola. ... | 2001 | 11222582 |
| rho is not essential for viability or virulence in staphylococcus aureus. | we have identified the gene for transcription termination factor rho in staphylococcus aureus. deletion of rho in s. aureus reveals that it is not essential for viability or virulence. we also searched the available bacterial genomic sequences for homologs of rho and found that it is broadly distributed and highly conserved. exceptions include streptococcus pneumoniae, streptococcus pyogenes, mycoplasma genitalium, mycoplasma pneumoniae, ureaplasma urealyticum, and synechocystis sp. strain pcc68 ... | 2001 | 11257021 |
| bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16s ribosomal dna sequencing. | we investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. for this investigation, we developed a composite method based on analyses of pcr amplicons containing the ribosomal intergenic spacer (ris) and its flanking partial 16s rrna gene. community percent similarity was determined on the basis of ris length polymorphism. a community succession was evident in the lagoon, indicated by a progressive community transition through seven sam ... | 2001 | 11282606 |
| parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition. | the overproduction of essential amino acids by buchnera aphidicola, the primary bacterial mutualist of aphids, is considered an adaptation for increased production of nutrients that are lacking in aphids' diet of plant sap. given their shared role in host nutrition, amino acid biosynthetic genes of buchnera are expected to experience parallel changes in selection that depend on host diet quality, growth rate, and population structure. this study evaluates the hypothesis of parallel selection acr ... | 2001 | 11399154 |
| complete dna sequence of yersinia enterocolitica serotype 0:8 low-calcium-response plasmid reveals a new virulence plasmid-associated replicon. | the complete nucleotide sequence and organization of the yersinia enterocolitica serotype 0:8 low-calcium-response (lcr) plasmid, pyve8081, were determined. the 67,720-bp plasmid encoded all the genes known to be part of the lcr stimulon except for ylpa. eight of 13 intact open reading frames of unknown function identified in pyve8081 had homologues in yersinia pestis plasmid pcd1 or in y. enterocolitica serotype 0:9 plasmid pyve227. a region of approximately 17 kbp showed no dna identity to pcd ... | 2001 | 11402007 |
| mutualists and parasites: how to paint yourself into a (metabolic) corner. | eukaryotes have developed an elaborate series of interactions with bacteria that enter their bodies and/or cells. genome evolution of symbiotic and parasitic bacteria multiplying inside eukaryotic cells results in both convergent and divergent changes. the genome sequences of the symbiotic bacteria of aphids, buchnera aphidicola, and the parasitic bacteria of body louse and humans, rickettsia prowazekii, provide insights into these processes. convergent genome characteristics include reduction i ... | 2001 | 11412844 |
| effects of rice seed surface sterilization with hypochlorite on inoculated burkholderia vietnamiensis. | when a combination of hydrogen peroxide and hypochlorite was used to surface sterilize rice seeds, a 10(2)- to 10(4)-fold decrease in cfu was observed during the first 15 h after inoculation of the rice rhizosphere organism burkholderia vietnamiensis tvv75. this artifact could not be eliminated simply by rinsing the seeds, even thoroughly, with sterile distilled water. when growth resumed, a significant increase in the frequency of rifampin- and nalidixic acid-resistant mutants in the population ... | 2001 | 11425720 |
| genome size determination and coding capacity of sodalis glossinidius, an enteric symbiont of tsetse flies, as revealed by hybridization to escherichia coli gene arrays. | recent molecular characterization of various microbial genomes has revealed differences in genome size and coding capacity between obligate symbionts and intracellular pathogens versus free-living organisms. multiple symbiotic microorganisms have evolved with tsetse fly, the vector of african trypanosomes, over long evolutionary times. although these symbionts are indispensable for tsetse fecundity, the biochemical and molecular basis of their functional significance is unknown. here, we report ... | 2001 | 11443086 |
| non-canonical mechanism for translational control in bacteria: synthesis of ribosomal protein s1. | translation initiation region (tir) of the rpsa mrna encoding ribosomal protein s1 is one of the most efficient in escherichia coli despite the absence of a canonical shine-dalgarno-element. its high efficiency is under strong negative autogenous control, a puzzling phenomenon as s1 has no strict sequence specificity. to define sequence and structural elements responsible for translational efficiency and autoregulation of the rpsa mrna, a series of rpsa'-'lacz chromosomal fusions bearing various ... | 2001 | 11483525 |
| the process of genome shrinkage in the obligate symbiont buchnera aphidicola. | very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. to examine the process of genome reduction, the tiny genome of the endosymbiont buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene o ... | 2001 | 11790257 |
| genome interdependence in insect-bacterium symbioses. | symbioses between unicellular and multicellular organisms have contributed significantly to the evolution of life on earth. as exemplified by several studies of bacterium-insect symbioses, modern genomic techniques are providing exciting new information about the molecular basis and the biological roles of these complex relationships, revealing for instance that symbionts have lost many genes for functions that are provided by the host, but that they can provide amino acids that the host cannot ... | 2001 | 11790259 |
| the hemk gene in escherichia coli encodes the n(5)-glutamine methyltransferase that modifies peptide release factors. | class 1 peptide release factors (rfs) in escherichia coli are n(5)-methylated on the glutamine residue of the universally conserved ggq motif. one other protein alone has been shown to contain n(5)-methylglutamine: e.coli ribosomal protein l3. we identify the l3 methyltransferase as yfcb and show that it methylates ribosomes from a yfcb strain in vitro, but not rf1 or rf2. hemk, a close orthologue of yfcb, is shown to methylate rf1 and rf2 in vitro. hemk is immediately downstream of and co-expre ... | 2002 | 11847124 |
| selection in the evolution of gene duplications. | gene duplications have a major role in the evolution of new biological functions. theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. | 2002 | 11864370 |
| the nucleotide sequence of shiga toxin (stx) 2e-encoding phage phip27 is not related to other stx phage genomes, but the modular genetic structure is conserved. | in this study we determined the complete nucleotide sequence of shiga toxin 2e-encoding bacteriophage phi p27, isolated from the shiga toxin-producing escherichia coli patient isolate 2771/97. phi p27 is integrated as a prophage in the chromosomal yece gene. this integration generates identity segments of attl and attr sites with lengths of 11 nucleotides. the integrated prophage genome has a size of 42,575 bp. we identified 58 open reading frames (orfs), each with a length of >150 nucleotides. ... | 2002 | 11895953 |
| extensive domain shuffling in transcription regulators of dna viruses and implications for the origin of fungal apses transcription factors. | viral dna-binding proteins have served as good models to study the biochemistry of transcription regulation and chromatin dynamics. computational analysis of viral dna-binding regulatory proteins and identification of their previously undetected homologs encoded by cellular genomes might lead to a better understanding of their function and evolution in both viral and cellular systems. | 2002 | 11897024 |
| lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. | glutathione is found primarily in eukaryotes and in gram-negative bacteria. it has been proposed that eukaryotes acquired the genes for glutathione biosynthesis from the alpha-proteobacterial progenitor of mitochondria. to evaluate this, we have used bioinformatics to analyze sequences of the biosynthetic enzymes gamma-glutamylcysteine ligase and glutathione synthetase. | 2002 | 12049666 |
| secondary (gamma-proteobacteria) endosymbionts infect the primary (beta-proteobacteria) endosymbionts of mealybugs multiple times and coevolve with their hosts. | mealybugs (hemiptera, coccoidea, pseudococcidae) are plant sap-sucking insects that have within their body cavities specialized cells containing prokaryotic primary endosymbionts (p-endosymbionts). the p-endosymbionts have the unusual property of containing within their cytoplasm prokaryotic secondary endosymbionts (s-endosymbionts) [c. d. von dohlen, s. kohler, s. t. alsop, and w. r. mcmanus, nature (london) 412:433-436, 2001]. four-kilobase fragments containing 16s-23s ribosomal dna (rdna) wer ... | 2002 | 12088994 |
| the genetic properties of the primary endosymbionts of mealybugs differ from those of other endosymbionts of plant sap-sucking insects. | mealybugs (hemiptera, coccoidea, pseudococcidae), like aphids and psyllids, are plant sap-sucking insects that have an obligate association with prokaryotic endosymbionts that are acquired through vertical, maternal transmission. we sequenced two fragments of the genome of tremblaya princeps, the endosymbiont of mealybugs, which is a member of the beta subdivision of the proteobacteria. each of the fragments (35 and 30 kb) contains a copy of 16s-23s-5s rrna genes. a total of 37 open reading fram ... | 2002 | 12088995 |
| 50 million years of genomic stasis in endosymbiotic bacteria. | comparison of two fully sequenced genomes of buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. in contrast, the genomes of their closest free-living relatives, escherichia coli and salmonella spp., are more than 2000-fold more labile in content and g ... | 2002 | 12089438 |
| tissue localization of the endosymbiotic bacterium "candidatus blochmannia floridanus" in adults and larvae of the carpenter ant camponotus floridanus. | the distribution of endosymbiotic bacteria in different tissues of queens, males, and workers of the carpenter ant camponotus floridanus was investigated by light and electron microscopy and by in situ hybridization. a large number of bacteria could be detected in bacteriocytes within the midguts of workers, young virgin queens, and males. large amounts of bacteria were also found in the oocytes of workers and queens. in contrast, bacteria were not present in oocyte-associated cells or in the sp ... | 2002 | 12200264 |
| type iii secretion systems and the evolution of mutualistic endosymbiosis. | the view that parasites can develop cooperative symbiotic relationships with their hosts is both appealing and widely held; however, there is no molecular genetic evidence of such a transition. here we demonstrate that a mutualistic bacterial endosymbiont of grain weevils maintains and expresses inv/spa genes encoding a type iii secretion system homologous to that used for invasion by bacterial pathogens. phylogenetic analyses indicate that inv/spa genes were present in presymbiotic ancestors of ... | 2002 | 12213957 |
| acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. | endosymbionts, which are widely observed in nature, have undergone reductive genome evolution because of their long-term intracellular lifestyle. here we compared the complete genome sequences of two different endosymbionts, buchnera and a protist mitochondrion, with their close relatives to study the evolutionary rates of functional genes in endosymbionts. the results indicate that the rate of amino acid substitution is two times higher in symbionts than in their relatives. this rate increase w ... | 2002 | 12235368 |
| asymmetric directional mutation pressures in bacteria. | when there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of dna, the average nucleotide composition is theoretically expected to be a = t and g = c within each strand. deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands. by focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced b ... | 2002 | 12372146 |
| genome evolution in bacterial endosymbionts of insects. | many insect species rely on intracellular bacterial symbionts for their viability and fecundity. large-scale dna-sequence analyses are revealing the forces that shape the evolution of these bacterial associates and the genetic basis of their specialization to an intracellular lifestyle. the full genome sequences of two obligate mutualists, buchnera aphidicola of aphids and wigglesworthia glossinidia of tsetse flies, reveal substantial gene loss and an integration of host and symbiont metabolic f ... | 2002 | 12415315 |
| extremely low levels of genetic polymorphism in endosymbionts (buchnera) of aphids (pemphigus). | molecular evolutionary studies have suggested that vertically transmitted endosymbionts are subject to accumulation of deleterious mutations through genetic drift. predictions of this hypothesis for patterns of intraspecific polymorphism were borne out in the single relevant study available, on the symbiont buchnera aphidicola of uroleucon ambrosiae. in order to examine the generality of this result, we surveyed dna sequence variation in buchnera of the distantly related aphid, pemphigus obesiny ... | 2002 | 12453247 |
| the secb chaperone is bifunctional in serratia marcescens: secb is involved in the sec pathway and required for hasa secretion by the abc transporter. | hasa is the secreted hemophore of the heme acquisition system (has) of serratia marcescens. it is secreted by a specific abc transporter apparatus composed of three proteins: hasd, an inner membrane abc protein; hase, another inner membrane protein; and hasf, a tolc homolog. except for hasf, the structural genes of the has system are encoded by an iron-regulated operon. in previous studies, this secretion system has been reconstituted in escherichia coli, where it requires the presence of the se ... | 2003 | 12486043 |
| a polyphosphate kinase (ppk2) widely conserved in bacteria. | synthesis of inorganic polyphosphate (poly p) from the terminal phosphate of atp is catalyzed reversibly by poly p kinase (ppk, now designated ppk1) initially isolated from escherichia coli. ppk1 is highly conserved in many bacteria, including some of the major pathogens such as pseudomonas aeruginosa. in a null mutant of p. aeruginosa lacking ppk1, we have discovered a previously uncharacterized ppk activity (designated ppk2) distinguished from ppk1 by the following: synthesis of poly p from gt ... | 2002 | 12486232 |
| algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. | comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (hgt), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more common in evolution. this complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task. | 2003 | 12515582 |
| the swiss-prot protein knowledgebase and its supplement trembl in 2003. | the swiss-prot protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the life sciences. each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. detailed expertise that goes beyond the scope of swiss-prot is made available via direct links to specialised databases. swiss-p ... | 2003 | 12520024 |
| reductive genome evolution in buchnera aphidicola. | we have sequenced the genome of the intracellular symbiont buchnera aphidicola from the aphid baizongia pistacea. this strain diverged 80-150 million years ago from the common ancestor of two previously sequenced buchnera strains. here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. as a consequence, the genome assembly unveiled intrapopulational variation, consisting of approximately 1,200 polymorphic sites. comparison of the 618-kb (kbp) g ... | 2003 | 12522265 |
| prokaryotic utilization of the twin-arginine translocation pathway: a genomic survey. | the twin-arginine translocation (tat) pathway, which has been identified in plant chloroplasts and prokaryotes, allows for the secretion of folded proteins. however, the extent to which this pathway is used among the prokaryotes is not known. by using a genomic approach, a comprehensive list of putative tat substrates for 84 diverse prokaryotes was established. strikingly, the results indicate that the tat pathway is utilized to highly varying extents. furthermore, while many prokaryotes use thi ... | 2003 | 12562823 |
| facultative bacterial symbionts in aphids confer resistance to parasitic wasps. | symbiotic relationships between animals and microorganisms are common in nature, yet the factors controlling the abundance and distributions of symbionts are mostly unknown. aphids have an obligate association with the bacterium buchnera aphidicola (the primary symbiont) that has been shown to contribute directly to aphid fitness. in addition, aphids sometimes harbor other vertically transmitted bacteria (secondary symbionts), for which few benefits of infection have been previously documented. ... | 2003 | 12563031 |
| leucine biosynthesis in fungi: entering metabolism through the back door. | after exploring evolutionary aspects of branched-chain amino acid biosynthesis, the review focuses on the extended leucine biosynthetic pathway as it operates in saccharomyces cerevisiae. first, the genes and enzymes specific for the leucine pathway are considered: leu4 and leu9 (encoding the alpha-isopropylmalate synthase isoenzymes), leu1 (isopropylmalate isomerase), and leu2 (beta-isopropylmalate dehydrogenase). emphasis is given to the unusual distribution of the branched-chain amino acid pa ... | 2003 | 12626680 |
| why are the genomes of endosymbiotic bacteria so stable? | the comparative analysis of three strains of the endosymbiotic bacterium buchnera aphidicola has revealed high genome stability associated with an almost complete absence of chromosomal rearrangements and horizontal gene transfer events during the past 150 million years. the loss of genes involved in dna uptake and recombination in the initial stages of endosymbiosis probably underlies this stability. gene loss, which was extensive during the initial steps of buchnera evolution, has continued in ... | 2003 | 12683967 |
| comparing bacterial genomes through conservation profiles. | we constructed two-dimensional representations of profiles of gene conservation across different genomes using the genome of escherichia coli as a model. these profiles permit both the visualization at the genome level of different traits in the organism studied and, at the same time, reveal features related to the genomes analyzed (such as defective genomes or genomes that lack a particular system). conserved genes are not uniformly distributed along the e. coli genome but tend to cluster toget ... | 2003 | 12695324 |
| an appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction. | an exhaustive search for shortly spaced repeats in 74 bacterial chromosomes reveals that they are much more numerous than is usually acknowledged. these repeats were divided into five classes: close repeats (crs), tandem repeats (trs), simple sequence repeats (ssrs), spaced interspersed direct repeats, and "others." crs are widespread and constitute the most abundant class, particularly in coding sequences. the other classes are less frequent, but each individual element shows a higher potential ... | 2003 | 12743022 |
| low and homogeneous copy number of plasmid-borne symbiont genes affecting host nutrition in buchnera aphidicola of the aphid uroleucon ambrosiae. | the bacterial endosymbiont of aphids, buchnera aphidicola, often provides amino acids to its hosts. plasmid amplification of leucine (leuabcd) and tryptophan (trpeg) biosynthesis genes may be a mechanism by which some buchnera over-produce these nutrients. we used quantitative polymerase chain reaction to assess the leuabcd/trpeg copy variability within uroleucon ambrosiae, an aphid with a wide diet breadth and range. both leuabcd and trpeg abundances are: (i) similar for aphids across 15 popula ... | 2003 | 12753227 |
| crystal structure of trna(m1g37)methyltransferase: insights into trna recognition. | trna(m(1)g37)methyltransferase (trmd) catalyzes the transfer of a methyl group from s-adenosyl-l- methionine (adomet) to g(37) within a subset of bacterial trna species, which have a g residue at the 36th position. the modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. here we report four crystal structures of trmd from haemophilus influenzae, as binary complexes with either adomet or s-adenosyl-l-homocy ... | 2003 | 12773376 |
| consequences of reductive evolution for gene expression in an obligate endosymbiont. | the smallest cellular genomes are found in obligate symbiotic and pathogenic bacteria living within eukaryotic hosts. in comparison with large genomes of free-living relatives, these reduced genomes are rearranged and have lost most regulatory elements. to test whether reduced bacterial genomes incur reduced regulatory capacities, we used full-genome microarrays to evaluate transcriptional response to environmental stress in buchnera aphidicola, the obligate endosymbiont of aphids. the 580 genes ... | 2003 | 12791133 |
| developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through hisf. | hish-hisf is a multidomain globular protein complex; hish is a class i glutamine amidotransferase that hydrolyzes glutamine to form ammonia, and hisf is a (beta/alpha)8 barrel cyclase that completes the ring formation of imidizole glycerol phosphate synthase. together, hish and hisf form a glutamine amidotransferase that carries out the fifth step of the histidine biosynthetic pathway. recently, it has been suggested that the (beta/alpha)8 barrel participates in a novel function: to channel ammo ... | 2003 | 12799468 |
| the genome sequence of blochmannia floridanus: comparative analysis of reduced genomes. | bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. we present the complete genome sequence of blochmannia floridanus, the primary endosymbiont of carpenter ants. although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. remarkably, these bacteria lack all known ge ... | 2003 | 12886019 |
| gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. | lineage-specific gene loss, to a large extent, accounts for the differences in gene repertoires between genomes, particularly among eukaryotes. we derived a parsimonious scenario of gene losses for eukaryotic orthologous groups (kogs) from seven complete eukaryotic genomes. the scenario involves substantial gene loss in fungi, nematodes, and insects. based on this evolutionary scenario and estimates of the divergence times between major eukaryotic phyla, we introduce a numerical measure, the pro ... | 2003 | 14525925 |
| a genomic perspective on nutrient provisioning by bacterial symbionts of insects. | many animals show intimate interactions with bacterial symbionts that provision hosts with limiting nutrients. the best studied such association is that between aphids and buchnera aphidicola, which produces essential amino acids that are rare in the phloem sap diet. genomic studies of buchnera have provided a new means for inferring metabolic capabilities of the symbionts and their likely contributions to hosts. despite evolutionary reduction of genome size, involving loss of most ancestral gen ... | 2003 | 14527994 |
| developmental origin and evolution of bacteriocytes in the aphid-buchnera symbiosis. | symbiotic relationships between bacteria and insect hosts are common. although the bacterial endosymbionts have been subjected to intense investigation, little is known of the host cells in which they reside, the bacteriocytes. we have studied the development and evolution of aphid bacteriocytes, the host cells that contain the endosymbiotic bacteria buchnera aphidicola. we show that bacteriocytes of acyrthosiphon pisum express several gene products (or their paralogues): distal-less, ultrabitho ... | 2003 | 14551917 |
| the genome of nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. | the hyperthermophile nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon ignicoccus. ribosomal protein and rrna-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom nanoarchaeota. the n. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. it is the smallest microbial genome seque ... | 2003 | 14566062 |
| tracing the evolution of gene loss in obligate bacterial symbionts. | the gamma-proteobacterial symbionts of insects are a model group for comparative studies of genome reduction. the phylogenetic proximity of these reduced genomes to the larger genomes of well-studied free-living bacteria has enabled reconstructions of the process by which genes and dna are lost. three genome sequences are now available for buchnera aphidicola. analyses of buchnera genomes in comparison with those of related enteric bacteria suggest that extensive changes including large deletion ... | 2003 | 14572545 |
| automatic annotation of protein function based on family identification. | although genomes are being sequenced at an impressive rate, the information generated tells us little about protein function, which is slow to characterize by traditional methods. automatic protein function annotation based on computational methods has alleviated this imbalance. the most powerful current approach for inferring the function of new proteins is by studying the annotations of their homologues, since their common origin is assumed to be reflected in their structure and function. unfo ... | 2003 | 14579359 |