Molecular characterization of Brucella abortus chromosome II recombination

Large-scale genomic rearrangements including inversions, deletions, and duplications are significant in bacterial evolution. The recently completed Brucella melitensis 16M and Brucella suis 1330 genomes have facilitated the investigation of such events in the Brucella spp. Suppressive subtractive hybridization (SSH) was employed in identifying genomic differences between B. melitensis 16M and Brucella abortus 2308. Analysis of 45 SSH clones revealed several deletions on chromosomes of B. abortus and B. melitensis that encoded proteins of various metabolic pathways. A 640-kb inversion on chromosome II of B. abortus has been reported previously (S. Michaux Charachon, G. Bourg, E. Jumas Bilak, P. Guigue Talet, A. Allardet Servent, D. O'Callaghan, and M. Ramuz, J. Bacteriol. 179:3244-3249, 1997) and is further described in this study. One end of the inverted region is located on a deleted TATGC site between open reading frames BMEII0292 and BMEII0293. The other end inserted at a GTGTC site of the cyclic-di-GMP phosphodiesterase A (PDEA) gene (BMEII1009), dividing PDEA into two unequal DNA segments of 160 and 977 bp. As a consequence of inversion, the 160-bp segment that encodes the N-terminal region of PDEA was relocated at the opposite end of the inverted chromosomal region. The splitting of the PDEA gene most likely inactivated the function of this enzyme. A recombination mechanism responsible for this inversion is proposed.     

Molecular characterization of L2 lipoxygenase from maize embryos

We investigated the expression and accumulation pattern of lipoxygenaseisoforms throughout the maize plant life. Two forms of lipoxygenase L1and L2 have been identified as acidic proteins of 100 kDa (pI 6.4) and90 kDa (pI 5.5-5.7) which accumulate in dry embryos and in variousorgans of maize seedlings. In young embryos, only the L2 form wasdetected and accumulation of L2 mRNA decreased during embryodevelopment. Identification of lipoxygenases from in vivo and in vitro synthesized proteins indicates that similar levels of both L1and L2 forms accumulated during treatment with abscisic acid, (ABA)gibberellic acid (GA₃) and jasmonic acid (JA). However,differences in the activity of both enzymes were detected. By using anantiserum directed against purified L2 we isolated and characterized apartial cDNA clone of maize embryos encoding a lipoxygenase. The deducedamino acid sequence of L2 cDNA shares 78% identity with the rice L2protein, and 51-56% identity with lipoxygenases from thedicotyledonous plants soybean and Arabidopsis/. DNA blotanalysis indicated that maize contains a family of lipoxygenase geneswhich are presently being characterized.     

Geographic distribution and recombination of genomic fragments on the short arm of chromosome 2 of Arabidopsis thaliana

Abstract: Range expansion from Pleistocene refugia and anthropogenic influences contribute to the present distribution pattern of Arabidopsis thaliana. We scored a genome-wide set of CAPSs and found two markers with an east-west geographic distribution across the Eurasian range of the species. Regions around the two SNPs were sequenced in 98 accessions, including newly collected plants from Middle Asia and Western Siberia. These regions correspond to a gene (∼ 1500 bp) and a non-coding region (∼ 500 bp) 300 kbp apart on chromosome 2. Nucleotide diversities, π, of the two sequenced fragments were 0.0032 and 0.0130. The haplotypes of both sequences belonged to one of two groups: a rather uniform "Asian" and a more variable "European" haplotype group, on the basis of non-disjunct clusters of SNPs. Recombination between "Asian" and "European" haplotypes occurs where they meet. Especially in the "European" haplotype, many rare SNP variants representing independent mutations are scattered among the shared haplotype-specific SNPs. This agrees with previous suggestions of two large haplotype groups in A. thaliana and the post-glacial colonization of central Europe from the east and the west. A clear correlation between climatic factors and the haplotype distribution may reflect the dispersal history rather than local climate adaptation. The pattern of SNP variation within the contiguous sequences explains why only a minority of SNPs selected across the genome show evidence of this geographic pattern.     

Effect of trisomy 6 on recombination in chromosome 9 of maize

The effect of an additional chromosome 6 upon recombination in chromosome 9 was investigated in maize. Trisomic 6 plants and their disomic sibs, heterozygous for three loci of chromosome 9 (yg, sh and wx), were testcrossed, and recombination in the regions yg–sh and sh–wx was analyzed. Single exchanges in the sh–wx region and double exchanges were more frequent in trisomics, particularly in female flowers.——In reciprocal testcrosses, higher male crossover rates were found for the sh–wx region, and the difference was enhanced in trisomic 6 plants.     

Molecular characterization of a pericentric inversion in mouse chromosome 8 implicates telomeres as promoters of meiotic recombination

A hot spot of meiotic recombination has been found in males on murine chromosome 8 using nonisotopic hybridization of a series of probes to mitotic and meiotic chromosomes. The sequences responsible for this enhanced recombination are the telomeric repeats. Mice both normal and hetero- or homozygous for a pericentric inversion, In(8) 1 Rl, were analyzed. The inversion subdivides chromosome 8 into three discreet regions: (1) a fraction of the micro short arm that contains 30–150 kb of telomeric sequences and only about one-fifth of the contiguous minor-satellite sequences (approximately 200 kb); (2) the inverted region; and (3) the noninverted distal two-thirds of the chromosome. In 70 spermatocytes from inversion heterozygotes, examined by electron microscopy, synapsis of the inverted region was complete but entirely nonhomologous. Nonhomologous synapsis persists from initiation of synaptonemal complex formation in zygonema/early pachynema until dissolution in late pachynema. This nonhomologous synapsis also suppresses crossing over within the inverted segment. The opportunity for proximal homologous recombination is thus restricted to the roughly 250 kb segment located between the short-arm break and the end of the bivalent. Nonetheless, an extreme proximal chiasma was observed in 11% of the heterozygous chromosome-8 bivalents, 34% of the normal 8 bivalents and 35% of the homozygous inversion 8 bivalents from spermatocyte preparations. Since in the normal chromosomes all minor satellite sequences are adjacent to the telomere, while in the inversion chromosomes most of these sequences are transposed to an interstitial position without a corresponding shift in chiasma position, the minor-satellite sequences can be ruled out as promoters of recombination. Instead, the data suggest that it is the telomeric sequences that promote recombination, not just within the telomeric repeat itself, but quite frequently in sequences more than 250 kb away.by T. HassoldThis paper is dedicated to the memory of Barbara McClintock, whose early contributions on meiosis were as fundamental as her later ones on transposable elements.     

Effects of trans-acting genetic modifiers on meiotic recombination across the a1-sh2 interval of maize

Meiotic recombination rates are potentially affected by cis- and trans-acting factors, i.e., genotype-specific modifiers that do or do not reside in the recombining interval, respectively. Effects of trans modifiers on recombination across the approximately 140-kb maize a1-sh2 interval of chromosome 3L were studied in the absence of polymorphic cis factors in three genetically diverse backgrounds into which a sequence-identical a1-sh2 interval had been introgressed. Genetic distances across a1-sh2 varied twofold among genetic backgrounds. Although the existence of regions exhibiting high and low rates of recombination (hot and cold spots, respectively) was conserved across backgrounds, the absolute rates of recombination in these sequence-identical regions differed significantly among backgrounds. In addition, an intergenic hot spot had a higher rate of recombination as compared to the genome average rate of recombination in one background and not in another. Recombination rates across two genetic intervals on chromosome 1 did not exhibit the same relationships among backgrounds as was observed in a1-sh2. This suggests that at least some detected trans-acting factors do not equally affect recombination across the genome. This study establishes that trans modifier(s) polymorphic among genetic backgrounds can increase and decrease recombination in both genic and intergenic regions over relatively small genetic and physical intervals.     

Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.)

We investigate the interplay between genetic diversity and recombination in maize (Zea mays ssp. mays). Genetic diversity was measured in three types of markers: single-nucleotide polymorphisms, indels, and microsatellites. All three were examined in a sample of previously published DNA sequences from 21 loci on maize chromosome 1. Small indels (1-5 bp) were numerous and far more common than large indels. Furthermore, large indels (>100 bp) were infrequent in the population sample, suggesting they are slightly deleterious. The 21 loci also contained 47 microsatellites, of which 33 were polymorphic. Diversity in SNPs, indels, and microsatellites was compared to two measures of recombination: C (=4Nc) estimated from DNA sequence data and R based on a quantitative recombination nodule map of maize synaptonemal complex 1. SNP diversity was correlated with C (r = 0.65; P = 0.007) but not with R (r = -0.10; P = 0.69). Given the lack of correlation between R and SNP diversity, the correlation between SNP diversity and C may be driven by demography. In contrast to SNP diversity, microsatellite diversity was correlated with R (r = 0.45; P = 0.004) but not C (r = -0.025; P = 0.55). The correlation could arise if recombination is mutagenic for microsatellites, or it may be consistent with background selection that is apparent only in this class of rapidly evolving markers.     

The heterochromatic B chromosome of maize: the segments affecting recombination

The B chromosome of maize is known to increase recombination in specific regions of the genome. In an attempt to determine the portion of the B responsible for crossover enhancement, translocations between the B and A chromosomes were used to dissect the B into four distinct segments. The effects of the segments on crossing over were studied in a sensitive region composed of chromatin from chromosomes 3 and 9. The relatively euchromatic chromomeres terminating the B lacked enhancement activity, but the remaining segments, all of which possess large amounts of heterochromatin, were capable of elevating recombination. There was no localization of activity to a specific heterochromatic region, however.     

The supernumerary B chromosome of maize: drive and genomic conflict

The supernumerary B chromosome of maize is dispensable, containing no vital genes, and thus is variable in number and presence in lines of maize. In order to be maintained in populations, it has a drive mechanism consisting of nondisjunction at the pollen mitosis that produces the two sperm cells, and then the sperm with the two B chromosomes has a preference for fertilizing the egg as opposed to the central cell in the process of double fertilization. The sequence of the B chromosome coupled with B chromosomal aberrations has localized features involved with nondisjunction and preferential fertilization, which are present at the centromeric region. The predicted genes from the sequence have paralogues dispersed across all A chromosomes and have widely different divergence times suggesting that they have transposed to the B chromosome over evolutionary time followed by degradation or have been co-opted for the selfish functions of the supernumerary chromosome.     

Isolation and characterization of a genomic sequence of maize coding for a zein gene

Summary An EcoRI restriction endonuclease fragment of maize DNA coding for the 19,000 dalton zein protein was cloned in phage gt WES. The zein gene was identified by the electron microscopic analysis of RNA-DNA hybrids (R-loops) and DNA-DNA hybrids (D-loops). The R-loops were formed with poly(rA)-containing RNA isolated from 18 days post-pollination maize endosperm and showed no intervening non-hybridizing sequences (introns) within their 800 base length. A cDNA clone specific for the 19,000 dalton zein protein formed D-loops in the same position and orientation as the R-loops. The cloned fragment measured 4.4 kilobases (kb), the same size as an EcoRI fragment of maize DNA revealed by Southern analysis.     

Molecular and biochemical characterization of a cytokinin oxidase from maize

It is generally accepted that cytokinin oxidases, which oxidatively remove cytokinin side chains to produce adenine and the corresponding isopentenyl aldehyde, play a major role in regulating cytokinin levels in planta. Partially purified fractions of cytokinin oxidase from various species have been studied for many years, but have yet to clearly reveal the properties of the enzyme or to define its biological significance. Details of the genomic organization of the recently isolated maize (Zea mays) cytokinin oxidase gene (ckx1) and some of its Arabidopsis homologs are now presented. Expression of an intronless ckx1 in Pichia pastoris allowed production of large amounts of recombinant cytokinin oxidase and facilitated detailed kinetic and cofactor analysis and comparison with the native enzyme. The enzyme is a flavoprotein containing covalently bound flavin adenine dinucleotide, but no detectable heavy metals. Expression of the oxidase in maize tissues is described.     

A spontaneous derivative of abnormal chromosome 10 in maize

Summary A new type of abnormal chromosome 10 has been found among maize plants grown from seeds sent by Dr. Y. C. Ting of Harvard University. This chromosome deviates in its morphology from the orthodox abnormal chromosome 10 described by Rhoades (1952) and from the one described by Ting (1958b). It produces a low degree of neo-centric activity.Cytological observations of plants heterozygous for the new abnormal chromosome 10 and either an orthodox abnormal chromosome 10 or a normal one, have suggested that the new type was derived from an orthodox abnormal 10 through spontaneous breakage and loss of an important piece of its long arm. The delection involved the distal part of the long arm of orthodox abnormal chromosome 10, proximally limited by the third most distal dissimilar and prominent chromomere. This corresponds approximately to the extra segment at the end of orthodox abnormal chromosome 10 which remains unpaired in heterozygotes with the normal 10. It bears a large heterochromatic knob. The missing piece is a part of the larger fraction of the long arm of orthodox abnormal chromosome 10 that remains unaffected by crossingover in a heteromorphic bivalent having a normal chromosome 10 (telo-segment). The telo-segment has its proximal limit at the left of the most proximal of the 3 dissimilar chromomeres, probably between the R and Sr ₂ loci. It has been proposed that a factor or factors responsible for neo-centric activity are located in the portion of the telosegment between its proximal limit and the third most distal dissimilar chromomere (3 dissimilar chromomere region).Since the telo-segment of the orthodox abnormal 10 also bears a large knob in its distal half, it has been suggested that this segment has a dual role in neo-centric activity. The factor or factors located in the proximal piece of the telo-segment would stimulate over-abundance of fiber-forming substance, whereas local production of chromosomal fibers would depend ultimately on the knob's activity.If the large knob is absent, its role in neo-centric activity would be transferred to the next smaller and distally located hetero-chromatic mass, such as the knob-like body near the end of the new abnormal 10 which results from the fusion of the two most proximal prominent chromomeres of the telo-segment.This work has been partly done in the United States, under an I.C.A. — National Academy of Sciences fellowship.     

The molecular characterization of maize B chromosome specific AFLPs

INTRODUCTIONB chromosomes (Bs) are also called supernumer-ary chromosomes, accessory chromosomes or extrachromosomes. They are supernumerary to the stan-dard chromosome (A chromosomes) set, which arefound in hundreds of plants and animals. They areoften morphologicaIly distinct from A chromosomes,being sma1ler and more highly heterochromatic inmost cases. B chromosomes are inherited in a non-Mendelian wap They dO not pair with A chromo-somes, and exhibite meiotic and mitotic instabiIit…     

Evolutionary aspects of the genomic organization of rat chromosome 10

Using FISH and RH mapping a chromosomal map of rat chromosome 10 (RNO10) was constructed. Our mapping data were complemented by other published data and the final map was compared to maps of mouse and human chromosomes. RNO10 contained segments homologous to mouse chromosomes (MMU) 11, 16 and 17, with evolutionary breakpoints between the three segments situated in the proximal part of RNO10. Near one of these breakpoints (between MMU17 and 11) we found evidence for an inversion ancestral to the mouse that was not ancestral to the condition in the rat. Within each of the chromosome segments identified, the gene order appeared to be largely conserved. This conservation was particularly clear in the long MMU11-homologous segment. RNO10 also contained segments homologous to three human chromosomes (HSA5, 16, 17). However, within each segment of conserved synteny were signs of more extensive rearrangements. At least 13 different evolutionary breakpoints were indicated in the rat-human comparison. In contrast to what was found between rat and mouse, the rat-human evolutionary breaks were distributed along the entire length of RNO10.     

Molecular characterization of repetitive DNA sequences from a B chromosome

In the parasitic waspNasonia vitripennis, certain males carry a B chromosome, called PSR (paternal sex ratio), which causes the compaction and subsequent loss of the paternal chromosomes in fertilized eggs. BecauseNasonia are haplo-diploid, this leads to the production of all-male broods. Three families (PSR2, PSR18, PSR22) of related, tandemly repetitive DNAs were shown to be present solely on the PSR chromosome. These three families shared two conserved, palindromic ANA sequences, which may play a role in either PSR function or amplification of the tandem arrays. The tandem repeat family NV79 was determined to be present on the PSR chromosome as well as on at least one of the A chromosomes. This shared repeat as well as two repeat families (NV85, NV126) that were localized on the A chromosomes were detected in two sibling species ofN. vitripennis. NV79 and NV126 were also found in the more distantly related species,Trichomalopsis dubius.by H.F. Willard