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PubMed2006

Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis.

Genomic studies of natural variation in model organisms provide a bridge between molecular analyses of gene function and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana, recent studies of natural variation have led to the identification of genes underlying ecologically important complex traits, and provided new insights about the processes of genome evolution, geographic population structure, and the selective mechanisms shaping complex trait variation in natural populations. These advances illustrate the potential for a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to real-world environments.

Adaptation, Biological↗
PubMed2001

Genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader Pseudomonas sp. strain CA10.

The nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of the carAaAaBaBbCAc(ORF7)Ad genes of carbazole-degrading Pseudomonas sp. strain CA10 were determined. Thirty-two open reading frames (ORFs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (carAaAaBaBbCAcAdDFE) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. The high identities (68 to 83%) with the enzymes involved in 3-(3-hydroxyphenyl)propionic acid degradation were observed only for CarFE. This observation, together with the fact that two ORFs are inserted between carD and carFE, makes it quite likely that the carFE genes were recruited from another locus. In the 21-kb region upstream from carAa, aromatic-ring-hydroxylating dioxygenase genes (ORF26, ORF27, and ORF28) were found. Inductive expression in carbazole-grown cells and the results of homology searching indicate that these genes encode the anthranilate 1,2-dioxygenase involved in carbazole degradation. Therefore, these ORFs were designated antABC. Four homologous insertion sequences, IS5car1 to IS5car4, were identified in the neighboring regions of car and ant genes. IS5car2 and IS5car3 constituted the putative composite transposon containing antABC. One-ended transposition of IS5car2 together with the 5' portion of antA into the region immediately upstream of carAa had resulted in the formation of IS5car1 and ORF9. In addition to the insertion sequence-dependent recombination, gene duplications and presumed gene fusion were observed. In conclusion, through the above gene rearrangement, the novel genetic structure of the car gene cluster has been constructed. In addition, it was also revealed that the car and ant gene clusters are located on the megaplasmid pCAR1.

Amino Acid Sequence↗
PubMed1999

Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10.

Pseudomonas stutzeri strain AN10 is a naphthalene-degrading strain whose dissimilatory genes are chromosomally encoded. We sequenced a total of 11514bp including the entire naphthalene-degradation upper pathway (nah) of P. stutzeri AN10. Nine open reading frames, nahAaAbAcAdBFCED, encoding the enzymes for the degradation of naphthalene to salicylate, were identified. The nah genes of P. stutzeri AN10 have been compared with genes encoding isofunctional proteins from other Pseudomonas naphthalene-degradation upper pathways. The implications of the sequence homologies to the evolution of aromatic catabolic pathways are discussed. Our findings indicate that this entire catabolic module of P. stutzeri AN10 was recruited from other microorganisms and a short period of time has elapsed after its incorporation within the P. stutzeri AN10 genome. Comparisons also suggest the coexistence of two entire nah upper pathways in a host strain, and further recombination between them. These events could accelerate the evolution of modern catabolic pathways.

Amino Acid Sequence↗
PubMed2000

Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria.

The direct repeat region in Mycobacterium tuberculosis complex strains is composed of multiple direct variant repeats (DVRs), each of which is composed of a 36-bp direct repeat (DR) plus a nonrepetitive spacer sequence of similar size. It has been shown previously that clinical isolates show extensive polymorphism in the DR region by the variable presence of DVRs, and this polymorphism has been used in the epidemiology of tuberculosis. In an attempt to better understand the evolutionary scenario leading to polymorphic DR loci and to improve strain differentiation by spoligotyping, we characterized and compared the DNA sequences of the complete DR region and its flanking DNA of M. tuberculosis complex strains. We identified 94 different spacer sequences among 26 M. tuberculosis complex strains. No sequence homology was found between any of these spacers and M. tuberculosis DNA outside of the DR region or with any other known bacterial sequence. Although strains differed extensively in the presence or absence of DVRs, the order of the spacers in the DR locus was found to be well conserved. The data strongly suggest that the polymorphism in clinical isolates is the result of successive deletions of single discrete DVRs or of multiple contiguous DVRs from a primordial DR region containing many more DVRs than seen in present day isolates and that virtually no scrambling of DVRs took place during evolution. Because the majority of the novel spacer sequences identified in this study were confined to isolates of the rare Mycobacterium canettii taxon, the use of the novel spacers in spoligotyping led only to a slight improvement of strain differentiation by spoligotyping.

Animals↗
PubMedDate not supplied

Dorsal skin color patterns among southern right whales (Eubalaena australis): genetic basis and evolutionary significance.

Distribution and inheritance of dorsal skin color markings among two populations of southern right whales (Eubalaena australis) suggest that two genes influence dorsal skin color. The grey-morph and partial-grey-morph phenotypes (previously known as partial albino and grey-blaze, respectively) appear to be controlled by an X-linked gene, whereas the white blaze appears controlled by an autosomal gene (recessive phenotype). Calving intervals, calf size, and length of sighting history data suggest that partial-grey-morph, white-blaze, and black cows experience similar levels of reproductive success. Grey-morph cows (XgXg) are rare or absent in the two populations, but this was not unexpected given observed population frequencies of grey-morph males (XgY) and partial-grey-morph females (XGXg). The proportion of partial-grey-morph calves produced by black cows (XGXG) suggests that the reproductive success of grey-morph males was equal to that of black males, however, larger sample sizes are required to determine whether grey-morph males tend to have shorter sighting histories. The reproductive success of white-blaze males appeared similar to that of black males among whales off Argentina. There were significantly fewer white-blaze calves than expected off South Africa, which could be due to white-blaze males experiencing reduced reproductive success or to sighting blases that result in white-marked calves being misidentified as black calves. The relative frequencies of both types of dorsal color markings varied between the South African and Argentinian right whale populations, suggesting limited nuclear gene flow between these populations; analyses using other nuclear markers are under way to confirm the extent of gene flow.

Animals↗
PubMed1995

Imidazole acetol phosphate aminotransferase in Zymomonas mobilis: molecular genetic, biochemical, and evolutionary analyses.

hisH encodes imidazole acetol phosphate (IAP) aminotransferase in Zymomonas mobilis and is located immediately upstream of tyrC, a gene which codes for cyclohexadienyl dehydrogenase. A plasmid containing hisH was able to complement an Escherichia coli histidine auxotroph which lacked the homologous aminotransferase. DNA sequencing of hisH revealed an open reading frame of 1,110 bp, encoding a protein of 40,631 Da. The cloned hisH product was purified from E. coli and estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to have a molecular mass of 40,000 Da. Since the native enzyme had a molecular mass of 85,000 Da as determined by gel filtration, the active enzyme species must be a homodimer. The purified enzyme was able to transaminate aromatic amino acids and histidine in addition to histidinol phosphate. The existence of a single protein having broad substrate specificity was consistent with the constant ratio of activities obtained with different substrates following a variety of physical treatments (such as freeze-thaw, temperature inactivation, and manipulation of pyridoxal 5'-phosphate content). The purified enzyme did not require addition of pyridoxal 5'-phosphate, but dependence upon this cofactor was demonstrated following resolution of the enzyme and cofactor by hydroxylamine treatment. Kinetic data showed the classic ping-pong mechanism expected for aminotransferases. Km values of 0.17, 3.39, and 43.48 mM for histidinol phosphate, tyrosine, and phenylalanine were obtained. The gene structure around hisH-tyrC suggested an operon organization. The hisH-tyrC cluster in Z. mobilis is reminiscent of the hisH-tyrA component of a complex operon in Bacillus subtilis, which includes the tryptophan operon and aroE. Multiple alignment of all aminotransferase sequences available in the database showed that within the class I superfamily of aminotransferases, IAP aminotransferases (family I beta) are closer to the I gamma family (e.g., rat tyrosine aminotransferase) than to the I alpha family (e.g., rat aspartate aminotransferase or E. coli AspC). Signature motifs which distinguish the IAP aminotransferase family were identified in the region of the active-site lysine and in the region of the interdomain interface.

Amino Acid Sequence↗
PubMed1988

Evolutionary implication of genetic code deviations.

We formulate the following hypothesis: Life's origin may have occurred during the lower Archaean at a time when the environmental temperature was higher than it is at present. Preliminary consequences of this hypothesis are studied from the point of view of molecular evolution. We restrict our attention to implications regarding the genetic code. We conclude that alternative assignment of termination codons may be understood in terms of: (a) the elevated temperatures to which the progenote may initially have been exposed; and (b) the subsequent response of its genome to the opportunity provided by the eventual loss of hyperthermal genetic expression during a thermal transition (TT) period, which was triggered off by the evolution of the dynamic Earth.

Biological Evolution↗
PubMed1998

Evolutionary rate and genetic heterogeneity of human T-cell lymphotropic virus type II (HTLV-II) using isolates from European injecting drug users.

Seven new Italian and two new British HTLV-II isolates were obtained from injecting drug users and the entire long terminal repeat (LTR) region was sequenced. Restriction analysis showed that all the Italian isolates are of the IIb subtype, whereas the British isolates are of the IIa subtype. To understand whether the further differentiation of each two principal HTLV-II subtypes in several subgroups could be statistically supported by phylogenetic analysis, the neighbor-joining, parsimony, and maximum likelihood methods were used. The separation between IIa and IIb is very well supported by all three methods. At least two phylogenetic subgroups exist within the HTLV-IIa and at least three within the HTLV-IIb subtype. In the present analysis, no statistical support was obtained for additional phylogroups. Two particular subgroups seem interesting because they include all European and North American injecting drug user strains within the IIa and IIb subtypes, respectively. These data confirm that European HTLV-II infection among drug users is probably derived from North America. They also suggest that though a certain differentiation by restriction analysis in different subgroups is possible, carefully interpreted phylogenetic analyses remain necessary. Using the likelihood ratio test, a molecular clock for the drug user strains was calibrated. A fixation rate between 1.08 x 10(-4) and 2.7 x 10(-5) nucleotide substitutions per site per year was calculated for the IIa and IIb injecting drug user strains. This is the lowest fixation rate so far reported for RNA viruses, including for HIV, which typically range between 10(-2) and 10(-4).

Biological Evolution↗
PubMed1994

Evolutionary implications of genetic variations in the S1 gene of infectious bronchitis virus.

The large number of phenotypically distinct strains of infectious bronchitis virus (IBV) provide a broad genetic background for examining naturally occurring coronavirus variation. Comparisons of the published nucleotide sequence of S1 genes of strains isolated in Europe, Japan and the USA and four additional American strains described in this report identified 4 genetically distinct groups. The Dutch group was the most divergent sharing only about 60% identity with the American, Mass and European groups which were about 80% homologous with each other. Whereas the strains within the Mass, European and Dutch strains were at least 95% homologous, the strains within the American group were most variable, sharing about 80% identity. The hypervariable region (HVR) which tended to correlate with serotype extended from amino acid residue 53 to 148. In addition to the previously described putative recombination events in the S1 gene of PP14 and SE17, we have now described similar shifts in homology in the corresponding gene of the Gray, Holte, 6/82 (European strain), and Iowa strains. Although minor cross-over sites were identified in the more conserved 3' end at approximately nt 1000 and 1400, a frequently used hot-spot for recombination extended from nt 25 to a region immediately upstream of, but not including, the hypervariable region (HVR). In addition to point mutations, deletions, and insertions, recombination often involving Mass-like and Ark-like sequences, is a commonly used mechanism responsible for the evolution of IBV.

Amino Acid Sequence↗
PubMed2004

Genetic, biochemical and evolutionary facets of Xmrk-induced melanoma formation in the fish Xiphophorus.

Certain interspecific hybrids of the fish Xiphophorus spontaneously develop melanoma induced by the derepression of the Xmrk oncogene. Xmrk is a recent duplicate of an orthologue of the mammalian epidermal growth factor receptor gene Egfr. In addition to a specific overexpression in melanoma, amino-acid substitutions in the extracellular domain leading to ligand-independent dimerisation and constitutive autophosphorylation are responsible for the tumorigenic potential of Xmrk. The Xmrk receptor induces several signal transduction pathways mediating cell proliferation and resistance to apoptosis and initiating dedifferentiation. Moreover, Xmrk upregulates the expression of the secreted protein osteopontin, inducing an autocrine loop possibly allowing invasion and survival in the dermis as a first step in malignancy. Hence, Xmrk is able to induce pathways essential for a transformed phenotype. Some of these events are equivalent to those found downstream of the mammalian Egfr, but others have clearly evolved differently or are specific for pigment cells. Xmrk is potentially hazardous, nonessential and located in a very unstable genomic region. Nevertheless, Xmrk has been maintained under purifying selection in divergent Xiphophorus species. Hence, Xmrk has probably a beneficial function under certain conditions. The analysis of this function is a major challenge for future research in the Xiphophorus model.

Animals↗
PubMed2005

Evolutionary history, population genetics, and gene flow in the common rosefinch (Carpodacus erythrinus).

We analyzed sequences of two mitochondrial DNA gene regions (control region and ND2) from 186 specimens obtained from 17 Eurasian localities covering most of the distribution of the common rosefinch to assess phylogeographic structure. Populations possessed a high level of nucleotide diversity relative to many other Palearctic species, suggesting that rosefinch populations are relatively old and possess high effective sizes. Mismatch distributions suggested that many localities experienced past population expansions, which are older than those expected for post-Pleistocene climate warming and reforestation of Eurasia. Our Phi(st) analysis revealed that 12.4% of total genetic variation was distributed among localities owing in part to the existence of three incompletely isolated groups: southwestern (subspecies C. e. kubanensis), northeastern (subspecies C. e. grebnitskii), and northwestern (subspecies C. e. erythrinus and C. e. ferghanensis). The three groups are not reciprocally monophyletic which suggests that they were formed relatively recently. Gene flow among groups is restricted. Coalescence analysis indicated dispersal asymmetry.

Animals↗
PubMed2004

Evolutionary model with genetics, aging, and knowledge.

We represent a process of learning by using bit strings, where 1 bits represent the knowledge acquired by individuals. Two ways of learning are considered: individual learning by trial and error, and social learning by copying knowledge from other individuals or from parents in the case of species with parental care. The age-structured bit string allows us to study how knowledge is accumulated during life and its influence over the genetic pool of a population after many generations. We use the Penna model to represent the genetic inheritance of each individual. In order to study how the accumulated knowledge influences the survival process, we include it to help individuals to avoid the various death situations. Modifications in the Verhulst factor do not show any special feature due to its random nature. However, by adding years to life as a function of the accumulated knowledge, we observe an improvement of the survival rates while the genetic fitness of the population becomes worse. In this latter case, knowledge becomes more important in the last years of life where individuals are threatened by diseases. Effects of offspring overprotection and differences between individual and social learning can also be observed. Sexual selection as a function of knowledge shows some effects when fidelity is imposed.

Aging↗