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At least 19 recordsLinked to original sources

Evidence that banana bunchy top virus has a multiple component genome.

A 93 nucleotide sequence was found to be strongly conserved between two ssDNA genomic components of banana bunchy top virus (BBTV). Two outwardly extending degenerate primers were designed from this sequence and used in a polymerase chain reaction (PCR) with DNA extracted from purified BBTV virions. PCR amplified products consisting of at least seven distinct bands all approximately 1 kb and possibly representing full-length BBTV dsDNA were resolved. The PCR amplified products were cloned and the clones screened by restriction enzyme analysis. Four distinct restriction analysis groups were identified. These results confirm that the genome of BBTV contains at least five components and that it belongs to a previously undescribed group of plant viruses which may also contain subterranean clover stunt virus.

Base Sequence↗

Tomato yellow leaf curl virus: a whitefly-transmitted geminivirus with a single genomic component.

The genome of the tomato yellow leaf curl virus (TYLCV), a Bemisia tabaci-transmitted geminivirus, was cloned. All clones obtained were of one genomic molecule, analogous to DNA A of African cassava mosaic virus. Nucleotide sequence analysis of the TYLCV genome showed that it comprises 2787 nucleotides, encoding six open reading frames, two on the virion strand and four on the complementary strand. All of them have counterparts in other geminiviruses. Dimeric copies of the cloned viral genome were introduced into tomato plants by agroinoculation. Severe yellow leaf curl disease symptoms developed in all of them. Effective whitefly-mediated transmission of the virus from agroinoculated plants to test plants demonstrated that the cloned molecule carries all the information needed for virus replication, systemic infection, and transfer by whiteflies. Restriction and hybridization analyses of viral DNA forms in infected plants and viruliferous whiteflies did not support the presupposed existence of a second genomic component. This is the first report of a whitefly-transmitted geminivirus that possesses a single genomic molecule.

Animals↗

Transcription map of the B genome component of tomato golden mosaic virus and comparison with A component transcripts.

In a previous study, the bipartite genome of tomato golden mosaic virus (TGMV) was shown to be transcribed into at least six polyadenylated RNAs (G. Sunter, W.E. Gardiner, and D. M. Bisaro, 1989, Virology 170, 243-250). Two of these, a 1.3-kb complementary sense and a 0.9-kb viral sense transcript, were mapped to the B genome component of this geminivirus. The results of more detailed primer extension and S1 nuclease protection experiments presented here define the limits of the single transcription unit corresponding to the 0.9-kb RNA which spans the BR1 open reading frame (ORF). The data also demonstrate that complementary sense TGMV RNAs are more complex than indicated by our earlier studies. Analysis of the 1.3-kb BL1-specific RNA indicates that it is actually a family of distinct transcripts with different start sites. Three transcripts have 5' ends that map near the common region of DNA B and all of these start sites lie upstream of the BL1 ORF. Similar analysis of the 1.6-kb complementary sense AL1 RNA indicates that a complex set of transcripts also map to the analogous region of genome component A. Four transcripts have 5' ends that map near the common region but only one of these start sites is upstream of the initiation codon for the AL1 open reading frame (ORF). None of the transcripts appear to be processed. The possible significance of multiple transcripts in these regions of the TGMV genome is discussed, and the common region-proximal transcription units of the A and B genome components are compared.

Autoradiography↗

Infectivity and complete nucleotide sequence of the cloned genomic components of a bipartite squash leaf curl geminivirus with a broad host range phenotype.

Through cloning and molecular analysis we have identified two highly homologous bipartite geminiviruses as causing squash leaf curl disease. Mechanical and Agrobacterium-mediated inoculation of plants with cloned viral DNA components identified the two genomic components of SqLCV-E, a squash leaf curl virus with an unexpectedly broad host range for a whitefly-transmitted geminivirus. Nucleotide sequence analysis of the genome of this virus showed it to have the same bipartite component organization characteristic of other whitefly-transmitted geminiviruses. Sequence comparison with the genomic components of tomato golden mosaic virus and bean golden mosaic virus revealed a close evolutionary relationship with these two bipartite geminiviruses, with which SqLCV-E shares common hosts. These studies provide clear molecular evidence for the assignment of SqLCV to the subfamily of bipartite geminiviruses.

Base Sequence↗

African cassava mosaic virus DI DNA interferes with the replication of both genomic components.

Natural infections of the geminivirus African cassava mosaic virus (ACMV) are known to be associated with low levels of defective interfering (DI) DNAs. Recently it has been demonstrated that extrachromosomal copies of the DI DNA, mobilized and amplified from an integrated DI DNA dimer, can ameliorate ACMV symptoms in transformed Nicotiana benthamiana, providing a possible means for the control of cassava mosaic disease. To further understand the molecular basis of the interference phenomenon, we have compared the ability of ACMV and tomato golden mosaic virus (TGMV) genomic components to replicate in leaf discs derived from DI DNA-transformed and control plants. Results indicate that the ACMV DI DNA interferes with the replication of both genomic components of ACMV to a similar extent. TGMV DNA A replicates to normal levels in transformed leaf discs and plants because it is unable to mobilize and amplify ACMV DI DNA. Differences in the relative levels of ACMV genomic components in transformed leaf discs and plants are discussed in terms of DNA replication and the availability of the genomic components for spread throughout the plant.

Blotting, Southern↗

Efficient whitefly transmission of African cassava mosaic geminivirus requires sequences from both genomic components.

Clones of two subgroup III geminiviruses, the common strain of tomato golden mosaic virus (csTGMV) and African cassava mosaic virus originating from Kenya (ACMV-K), were shown to be non-transmissible by whitefiles. Lack of transmissibility of cloned ACMV-K was investigated by exchanging genomic components with a whitefly-transmissible ACMV isolate from Nigeria (ACMV-NOg). Neither pseudorecombinant was transmissible, indicating that defects in both genomic components contributed to the lack of transmissibility. Analysis of the acquisition of the pseudorecombinats by Bemisia tabaci indicated that accumulation of virus within the insect was DNA B dependent. Return of virus to plants was determined by DNA A, although the coat protein was essential for acquisition. Repeated passaging of both the wild strain of ACMV-NOg and the cloned virus led to loss of insect transmissibility of the wild isolate but not the cloned virus. Products encoded on both genomic components are required for transmission of bipartite geminiviruses by B. tabaci.

Animals↗

Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses.

Genomes of the four plant viruses of the genus Nanovirus consist of multiple circular single-stranded DNA components, each of which encodes a single protein. Protein phylogenies supported the hypothesis that faba bean necrotic yellows virus (FBNYV) and milk vetch disease virus (MDV) are sister taxa; that subterranean clover stunt virus (SCSV) branched next; and that banana bunchy top virus (BBTV) is an outgroup to the three other species. The phylogeny of replication (Rep) proteins indicate that this small viral multi-gene family has evolved by a process of duplication and subsequent loss of Rep-encoding genome components, analogous to the "birth-and-death" process of evolution which has been described in eukaryotic multi-gene families. By contrast, repeated recombinational events between components were found to have homogenized the non-coding portions of several components encoding unrelated components. For example, as result of recent recombination a portion of the non-coding region is virtually identical among SCSV components 1, 3, 4, 5, and 7. Thus, there is a process of concerted evolution of non-coding regions of Nanovirus genome components, which raises the possibility that certain non-coding regions are subject to functional constraint.

Base Sequence↗

DNA sequences essential for replication of the B genome component of tomato golden mosaic virus.

The genome of the geminivirus tomato golden mosaic virus (TGMV) is divided between two DNA components, designated A and B, which differ in sequence except for a 230-nucleotide common region. The A genome component is known to encode viral functions necessary for viral DNA replication, while the B genome component specifies functions necessary for spread of the virus through the infected plant. To identify cis-acting sequences required for viral DNA replication, several mutants were constructed by the introduction of small insertions into TGMV B at selected sites within and just outside the common region. Other mutants had the common region inverted or deleted. All of the mutants were tested for their effects on infectivity and DNA replication in whole plants and leaf discs. Our results indicate that the common region in its correct orientation is required for infectivity and for replication of TGMV B. Furthermore, the conserved hairpin loop sequence located within the TGMV common region and found in all geminiviruses is necessary for DNA replication, and may be part of the viral replication origin.

Base Sequence↗

Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed.

In spite of its short history of being an oil crop in China, the Chinese semi-winter rapeseed (Brassica napus L., 2n = 38, AACC) has been improved rapidly by intentional introgression of genomic components from Chinese B. rapa (2n = 20, AA). As a result, the Chinese semi-winter rapeseed has diversified genetically from the spring and winter rapeseed grown in the other regions such as Europe and North America. The objectives of this study were to investigate the roles of the introgression of the genomic components from the Chinese B. rapa in widening the genetic diversity of rapeseed and to verify the role of this introgression in the evolution of the Chinese rapeseed. Ten lines of the new type of rapeseed, which were produced by introgression of Chinese B. rapa to Chinese normal rapeseed, were compared for genetic diversity using amplified fragment length polymorphism (AFLP) with three groups of 35 lines of the normal rapeseed, including 9 semi-winter rapeseed lines from China, 9 winter rapeseed lines from Europe and 17 spring rapeseed lines from Northern Europe, Canada and Australia. Analysis of 799 polymorphic fragments revealed that within the groups, the new type rapeseed had the highest genetic diversity, followed by the semi-winter normal rapeseed from China. Spring and winter rapeseed had the lowest genetic diversity. Among the groups, the new type rapeseed group had the largest average genetic distance to the other three groups. Principal component analysis and cluster analysis, however, could not separate the new type rapeseed group from Chinese normal rapeseed group. Our data suggested that the introgression of Chinese B. rapa could significantly diversify the genetic basis of the rapeseed and play an important role in the evolution of Chinese rapeseed. The use of new genetic variation for the exploitation of heterosis in Brassica hybrid breeding is discussed.

Brassica napus↗

Cloning, restriction mapping and phylogenetic relationship of genomic components of MYMIV from Lablab purpureus.

The present work describes cloning of genomic components of whitefly transmitted geminivirus infecting Lablab purpureus syn. Dolichos lablab (commonly known as Dolichos bean or Hyacinth bean). The genome characterization using PCR with geminiviral degenerate primers and DNA sequencing were used to describe the bipartite virus associated with yellow mosaic disease of Dolichos lablab. Full-length DNA-A and DNA-B clones were obtained. The DNA-A sequence analysis showed that the isolate was similar to other Mungbean yellow mosaic India virus (MYMIV) isolates reported earlier. The nucleotide sequence analysis of the full-length DNA-A of virus isolate revealed more than 97% homology with Mungbean yellow mosaic India virus-[Cowpea] (AF481865), while the DNA-B also showed >95% homology with MYMIV-[Cp] (AF503580) and MYMIV-[Sb] (AY049771). The phylogenetic analysis of present isolate showed close relationship to legume geminiviruses. The nucleotide sequence analysis showed presence of six open reading frames (ORFs) in DNA-A, with 2 ORFs aligned in sense and 4 ORFs in antisense orientation. Similarly, DNA-B contained two open reading frames (ORFs), one in sense and another in antisense orientation.

Cloning, Molecular↗

Infectivity of nanovirus DNAs: induction of disease by cloned genome components of Faba bean necrotic yellows virus.

Circumstantial evidence suggests that the genome of Faba bean necrotic yellows virus (FBNYV), a nanovirus, consists of eight distinct, circular, single-stranded DNAs, each of about 1 kb and encoding only one protein. Here, the use of cloned full-length FBNYV DNAs for reproducing FBNYV-like symptoms in Vicia faba, the principal natural host of FBNYV, is reported. Characteristic symptoms of FBNYV infection were obtained in faba bean plants following biolistic DNA delivery or agroinoculation with all eight FBNYV DNAs. Although the eight different DNAs have been invariably detected in field samples infected with the various geographical FBNYV isolates, experimental infection with different combinations of fewer than eight DNAs also led to typical FBNYV symptoms. Even only five genome components, DNA-R, DNA-S, DNA-M, DNA-U1 and DNA-U2, were sufficient for inducing disease symptoms in V. faba upon agroinoculation. Symptomatic plants agroinoculated or bombarded with eight DNAs contained typical FBNYV virions; however, the virus was not transmitted by Aphis craccivora or Acyrthosiphon pisum, two efficient aphid vectors of FBNYV.

Animals↗

Absence of interaction of genomic components and complementation between Mungbean yellow mosaic India virus isolates in cowpea.

Agroinoculations were performed with DNA A and DNA B components of Mungbean yellow mosaic India virus (MYMIV) isolates differing in their infectivity on cowpea. Exchange of genomic components of the MYMIV isolates occurred in all the leguminous species but not in cowpea. Extremely low viral DNA accumulation and atypical leaf curl symptoms produced by reassortants in cowpea suggest barriers both for replication and systemic movement despite genetic similarity.

Base Sequence↗

Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.

The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs.

Base Composition↗

A single rep protein initiates replication of multiple genome components of faba bean necrotic yellows virus, a single-stranded DNA virus of plants.

Faba bean necrotic yellows virus (FBNYV) belongs to the nanoviruses, plant viruses whose genome consists of multiple circular single-stranded DNA components. Eleven distinct DNAs, 5 of which encode different replication initiator (Rep) proteins, have been identified in two FBNYV isolates. Origin-specific DNA cleavage and nucleotidyl transfer activities were shown for Rep1 and Rep2 proteins in vitro, and their essential tyrosine residues that catalyze these reactions were identified by site-directed mutagenesis. In addition, we showed that Rep1 and Rep2 proteins hydrolyze ATP, and by changing the key lysine residue in the proteins' nucleoside triphosphate binding sites, demonstrated that this ATPase activity is essential for multiplication of virus DNA in vivo. Each of the five FBNYV Rep proteins initiated replication of the DNA molecule by which it was encoded, but only Rep2 was able to initiate replication of all the six other genome components. Furthermore, of the five rep components, only the Rep2-encoding DNA was always detected in 55 FBNYV samples from eight countries. These data provide experimental evidence for a master replication protein encoded by a multicomponent single-stranded DNA virus.

Adenosine Triphosphatases↗

Characterization of a new family of tobacco highly repetitive DNA, GRS, specific for the Nicotiana tomentosiformis genomic component.

Members of a new family of highly repetitive DNA sequences called GRS were isolated from Nicotiana tabacum L. genomic DNA and characterized. Cloned, sequenced monomeric units (180-182 bp) of GRS exhibit properties characteristic of molecules that possess a stable curvature. The GRS family represents about 0.15% of total genomic DNA (10(4) copies per haploid genome) and could be derived from either Nicotiana tomentosiformis or Nicotiana otophora, two possible ancestors of the T genome of the amphidiploid N. tabacum. Sequence homology between the HRS60 (Koukalová et al. 1989) and the GRS family has been estimated to be 57%. In situ hybridization was used to localize GRS on mitotic chromosomes. Hybridization signals were obtained on five pairs of chromosomes at intercalary sites of the longer chromosome arms. The majority of GRS sequences appeared to be organized in tandem arrays and a minority were found to be dispersed through the genome in short clusters, interspersed with other types of DNA repeats, including 25S rDNA sequences. Several loci containing both GRS and HRS60 were also found. Such hybrid loci may indicate intergenomic transfer of the DNA in the amphidiploid N. tabacum. GRS sequences, like HRS60 (Fajkus et al. 1992), were found to specify the location of nucleosomes. The position of the nucleosome core has been mapped with respect to a conserved Mbol site in the GRS sequence and an oligo A/T tract is a major centre of the DNA curvature.

Base Sequence↗

Replication-independent expression of genome components and capsid protein of brome mosaic virus in planta: a functional role for viral replicase in RNA packaging.

To begin elucidation of the relationship between Brome mosaic virus (BMV) replication and encapsidation, we used a T-DNA-based Agrobacterium-mediated transient expression (agroinfiltration) system in Nicotiana benthamiana leaves to express either individual or desired pairs of the three genomic RNAs. The packaging competence of these RNAs into virions formed by the transiently expressed coat protein (CP) was analyzed. We found that in the absence of a functional replicase, assembled virions contained non-replicating viral RNAs (RNA1 or RNA2 or RNA3 or RNA1 + RNA3 or RNA2 + RNA3) as well as cellular RNAs. By contrast, virions assembled in the presence of a functional replicase contained only viral RNAs. To further elucidate the specificity exhibited by the functional viral replicase in RNA packaging, replication-defective RNA1 and RNA2 were constructed by deleting the 3' tRNA-like structure (3' TLS). Co-expression of TLS-less RNA1 and RNA2 with wt RNA3 resulted in efficient synthesis of subgenomic RNA4. Virions recovered from leaves co-expressing TLS-less RNA1 and RNA2 and either CP mRNA or wt RNA3 exclusively contained viral RNAs. These results demonstrated that packaging of BMV genomic RNAs is not replication dependent whereas expression of a functional viral replicase plays an active role in increasing specificity of RNA packaging.

Base Sequence↗

[Divergence patterns of banding sequences in different polytene chromosome arms reflect relatively independent evolution of different genome components].

Divergence patterns of the banding sequences from the chromosomal arms A, C, D, E, and F were compared in 63 species of the genus Chironomus. Evaluation of the number of breakpoints between the pairs of inverted banding sequences and the analysis of the lengths of the conserved segments in the chromosomal arms in the chironomid species examined showed that different arms evolved relatively independently and at different rates. No direct correlation between the arm length and the breakpoints number was observed. The length of the conservative segment was not fixed, but was arm-specific. Robustness and fidelity of the estimates of phylogenetic relationships between the species examined increased with the arm number, i.e., with the genome proportion included in the analysis.

Animals↗

Genomic components of carcinogenesis.

Many of the genes encoding growth factors, growth factor receptors, enzymes, and other effector molecules that regulate normal cell growth are designated protooncogenes. Oncogenes, those genes associated with cellular transformation, differ from their protooncogenic progenitors by being mutated, overexpressed, or expressed at inappropriate times or locations in the cell. One of the activities of growth factors is to prime cells to undergo programmed cell death, which is characterized by a series of morphologic changes called apoptosis. In normal cells, specific mediators must be activated or suppressed to bypass programmed cell death. In tumor cells, either the pathways leading to apoptosis are not functional or the mediators that normally "rescue" cells from this fate are overexpressed or constitutively activated. In addition to the biochemical pathways that drive cell division, there are others that limit cell proliferation; these, designated tumor suppressors, anti-oncogenes, or recessive oncogenes, must be inactivated in normal cells to allow passage through the cell cycle and cell proliferation. In contrast to oncogenes, which are overexpressed or activated in tumors, tumor-suppressor genes are frequently inactivated in tumor cells, either by mutation or deletion. Thus, in normal cells a series of checks and balances must be overcome to allow initiation and continuation of cell division. In tumors, these processes are aberrant, resulting in increased rates of cell division, increases in the proportion of cells in the cell cycle, or increased survival of activated cells. Therefore, tumor cells frequently accumulate genomic alterations, which may result in the activation of a particular array of oncogenes, the inactivation of specific tumor-suppressor genes, and the bypassing of programmed cell death. Trials of antitumor agents that act by exploiting the overexpression of oncogenes in tumors and of the biochemical pathways by which they mediate cell proliferation are currently underway.

Apoptosis↗