Publications

1977
Messing, J, Gronenborn B, Müller-Hill B, Hans Hopschneider P.  1977.  Filamentous coliphage M13 as a cloning vehicle: insertion of a HindII fragment of the lac regulatory region in M13 replicative form in vitro. Proceedings of the National Academy of Sciences of the United States of America. 74:3642-6. AbstractWebsite
A HindII restriction fragment comprising the Escherichia coli lac regulatory region and the genetic information for the alpha peptide of beta-galactosidase (beta-D-galactosidegalactohydrolase, EC. 3.2.1.23) has been inserted into 1 of the 10 Bsu I cleavage sites of M13 by blunt end ligation. A stable hybrid phage was isolated and identified by its ability to complement the lac alpha function. Further characterization of the hybrid phage includes retransformation studies, agarose gel electrophoresis, DNA-DNA hybridization, and heteroduplex mapping. The insertion point has been localized at 0.083 map unit on thewild-type circular map-i.e., within the intergenic region. The results prove that part of the intergenic region is nonessential and that the phage can be used as a cloning vehicle.
1978
1980
Heidecker, G, Messing J, Gronenborn B.  1980.  A versatile primer for DNA sequencing in the M13mp2 cloning system. Gene. 10:69-73. AbstractWebsite
A primer for DNA sequencing by the chain-termination method in the M13mp2 cloning system was constructed and amplified. The primer was isolated as an EcoRI/AluI restriction fragment. After conversion of the AluI end into an EcoRI end the fragment was cloned in pBR325 from which it can be recovered by cleavage with EcoRI. The primer hybridizes to the single-stranded DNA of the mature M13mp2 phage next to the site of insertion thereby directing DNA synthesis along the inserted DNA.
1981
Gardner, RC, Howarth AJ, Hahn P, Brown-Luedi M, Shepherd RJ, Messing J.  1981.  The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing. Nucleic acids research. 9:2871-88. AbstractWebsite
We have determined the complete primary structure (8031 base pairs) of an infectious clone of cauliflower mosaic virus strain CM1841. The sequence was obtained using the strategy of cloning shotgun restriction fragments in the sequencing vector M13mp7. Comparison of the CM1841 sequence with that published for another caMV strain (Strasbourg) reveals 4.4% changes, mostly nucleotide substitutions with a few small insertions and deletions. The six open reading frames in the sequence of the Strasbourg isolate are also present in CM1841.
Geraghty, D, Peifer MA, Rubenstein I, Messing J.  1981.  The primary structure of a plant storage protein: zein. Nucleic acids research. 9:5163-74. AbstractWebsite
The protein sequence of a representative of the zeins, the major storage proteins of maize, has been derived from the nucleotide sequence of a zein cDNA clone. This cDNA was sequence both by the Maxam and Gilbert and the M13-dideoxy techniques. The nucleotide sequence encompasses the non-translated 3' terminus of the mRNA, the entire coding sequence specifying both the mature zein protein and a small signal peptide, and a portion of the non-translated 5' region. The deduced amino acid composition and the amino-terminal amino acid sequence closely resemble those derived from chemical analysis of the zein protein fraction. The data presented represent the first complete amino acid sequence of a plant storage protein.
Messing, J, Crea R, Seeburg PH.  1981.  A system for shotgun DNA sequencing. Nucleic acids research. 9:309-21. AbstractWebsite
A multipurpose cloning site has been introduced into the gene for beta-galactosidase (beta-D-galactosidegalactohydrolase, EC 3.21.23) on the single-stranded DNA phage M13mp2 (Gronenborn, B. and Messing, J., (1978) Nature 272, 375-377) with the use of synthetic DNA. The site contributes 14 additional codons and does not affect the ability of the lac gene product to undergo intracistronic complementation. Two restriction endonuclease cleavage sites in the viral gene II were removed by single base-pair mutations. Using the new phage M13mp7, DNA fragments generated by cleavage with a variety of different restriction endonucleases can be cloned directly. The nucleotide sequences of the cloned DNAs can be determined rapidly by DNA synthesis using chain terminators and a synthetic oligonucleotide primer complementary to 15 bases preceeding the new array of restriction sites.
1982
Larson, R, Messing J.  1982.  Apple II software for M13 shotgun DNA sequencing. Nucleic acids research. 10:39-49. AbstractWebsite
A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is required for the hardware and the software is easily interchangeable between the growing number of interested researchers. Copies are available in ready to use form.
Hu, NT, Peifer MA, Heidecker G, Messing J, Rubenstein I.  1982.  Primary structure of a genomic zein sequence of maize. The EMBO journal. 1:1337-42. AbstractWebsite
The nucleotide sequence of a genomic clone (termed Z4 ) of the zein multigene family was compared to the nucleotide sequence of related cDNA clones of zein mRNAs. A tandem duplication of a 96-bp sequence is found in the genomic clone that is not present in the related cDNA clones. When the duplication is disregarded, the nucleotide sequence homology between Z4 and its related cDNAs was approximately 97%. The nucleotide sequence is also compared to other isolated cDNAs. No introns in the coding region of the zein gene are detected. The first nucleotide of a putative TATA box, TATAAATA , was located 88 nucleotides upstream of the first nucleotide of the first ATG codon which initiated the open reading frame. The first nucleotide of a putative CCAAT box, CAAAAT , appeared 45 nucleotides upstream of the first nucleotide of the zein cDNA clones in the 3' non-coding region also appeared in the genomic sequence at the same locations. The amino acid composition of the polypeptide specified by the Z4 nucleotide sequence is similar to the known composition of zein proteins.
Vieira, J, Messing J.  1982.  The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 19:259-68. AbstractWebsite
A series of plasmid vectors containing the multiple cloning site (MCS7) of M13mp7 has been constructed. In one of these vectors a kanamycin-resistance marker has been inserted into the center of the symmetrical MCS7 to yield a restriction-site-mobilizing element (RSM). The drug-resistance marker can be cleaved out of this vector with any of the restriction enzymes that recognize a site of the flanking sequences of the RSM to generate an RSM with either various sticky ends or blunt ends. These fragments can be used for insertion mutagenesis of any target molecule with compatible restriction sites. Insertion mutants are selected by their resistance to kanamycin. When the drug-resistance marker is removed with PstI, a small in-frame insertion can be generated. In addition, two new MCSs having single restriction sites have been formed by altering the symmetrical structure of MCS7. The resulting plasmids pUC8 and pUC9 allow one to clone doubly digested restriction fragments separately with both orientations in respect to the lac promoter. The terminal sequences of any DNA cloned in these plasmids can be characterized using the universal M13 primers.
Geraghty, DE, Messing J, Rubenstein I.  1982.  Sequence analysis and comparison of cDNAs of the zein multigene family. The EMBO journal. 1:1329-35. AbstractWebsite
The nucleotide sequence of two zein cDNAs in hybrid plasmids A20 and B49 have been determined. The insert in A20 is 921 bp long including a 5' non-coding region of 60 nucleotides, preceded by what is believed to be an artifactual sequence of 41 nucleotides, and a 3' non-coding region of 87 nucleotides. The B49 insert is 467 bp long and includes approximately one-half the protein coding sequence as well as a 3' non-coding region of 97 nucleotides. These sequences have been compared with the previously published sequence of another zein clone, A30 . A20 and A30 , both encoding 19 000 mol. wt. zeins , have approximately 85% homology at the nucleotide level. The B49 sequence, corresponding to a 22 000 mol. wt. zein, has approximately 65% homology to either A20 or A30 . All three zeins share common features including nearly identical amino acid compositions. In addition, the tandem repeats of 20 amino acids first seen in A30 are also present in A20 and B49 .
1983
Norrander, J, Kempe T, Messing J.  1983.  Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 26:101-6. AbstractWebsite
The restriction endonuclease cleavage sites for SphI and KpnI have been added to the lac cloning region of the phage vectors M13mp10 and M13mp11, using oligodeoxynucleotide-directed in vitro mutagenesis. Complementary deoxy 16-, 21- or 18-mers with the desired base changes were annealed to the M13mp DNA strand and extended with the Klenow fragment of DNA polymerase I. In adding these sites we have shown that this technique can be used as a general method for inserting sequences of DNA as well as introducing deletions and base pair changes.
1985
Norrander, JM, Vieira J, Rubenstein I, Messing J.  1985.  Manipulation and expression of the maize zein storage proteins in Escherichia coli. Journal of biotechnology. 2:157-175.Website
1988
Kirihara, JA, Hunsperger JP, Mahoney WC, Messing JW.  1988.  Differential expression of a gene for a methionine-rich storage protein in maize. Molecular & general genetics : MGG. 211:477-84. AbstractWebsite
A methionine-rich 10 kDa zein storage protein from maize was isolated and the sequence of the N-terminal 30 amino acids was determined. Based on the amino acid sequence, two mixed oligonucleotides were synthesized and used to probe a maize endosperm cDNA library. A full-length cDNA clone encoding the 10 kDa zein was isolated by this procedure. The nucleotide sequence of the cDNA clone predicts a polypeptide of 129 amino acids, preceded by a signal peptide of 21 amino acids. The predicted polypeptide is unique in its extremely high content of methionine (22.5%). The maize inbred line BSSS-53, which has increased seed methionine due to overproduction of this protein, was compared to W23, a standard inbred line. Northern blot analysis showed that the relative RNA levels for the 10 kDa zein were enhanced in developing seeds of BSSS-53, providing a molecular basis for the overproduction of the protein. Southern blot analysis indicated that there are one or two 10 kDa zein genes in the maize genome.
Kirihara, JA, Petri JB, Messing J.  1988.  Isolation and sequence of a gene encoding a methionine-rich 10-kDa zein protein from maize. Gene. 71:359-70. AbstractWebsite
We have isolated the gene encoding a methionine-rich 10-kDa zein protein from a lambda EMBL3 maize genomic 'mini' library of the inbred line BSSS-53 and determined its nucleotide sequence. The sequence matches perfectly with a cDNA clone from the inbred line W22 (which has the same restriction fragment length polymorphism as many inbred lines tested) indicating that we have isolated a functional storage protein gene that is very conserved in maize. This comparison also excludes any splicing of any precursor mRNA and therefore any presence of introns. A number of potential regulatory sequences have been located in the flanking regions. The 10-kDa-zein gene represents the last size class in the zein multigene family to be characterized. Its structure allows us now to re-examine the relationship of all the zein proteins and also to compare the structure of a new class of storage proteins that are rich in methionine, an essential amino acid in livestock fodder.
1989
1991
Heidecker, G, Chaudhuri S, Messing J.  1991.  Highly clustered zein gene sequences reveal evolutionary history of the multigene family. Genomics. 10:719-32. AbstractWebsite
We have determined the nucleotide sequences of zein cDNA clones ZG14, ZG15, and ZG35. The three clones have 95 to 98% homology to the previously published sequence of clone A20, and 84% homology to sequences of the zein subfamily A30. Comparison of all sequences of the A30 and A20 subfamilies highlights the following features: the 5' nontranslated regions are 68 and 57 nucleotides in length for the A20- and A30-like mRNAs, respectively, and contain at least three repeats of the consensus sequence ACGAACAAta/gG; the majority of these genes are highly clustered as judged from pulsed-field gel electrophoresis of high molecular weight maize DNA. Furthermore, we discuss a model for the evolution of the multigene family which stresses the special importance of unequal crossingover and gene conversion in this system.
Messing, J, Fisher H.  1991.  Maternal effect on high methionine levels in hybrid corn. Journal of biotechnology. 21:229-237.Website
Cruz-Alvarez, M, Kirihara JA, Messing J.  1991.  Post-transcriptional regulation of methionine content in maize kernels. Molecular & general genetics : MGG. 225:331-9. AbstractWebsite
Message levels for a methionine-rich 10 kDa zein were determined in three inbred lines of maize and their reciprocal crosses at various stages during endosperm development. Inbred line BSSS-53, which overexpresses the 10 kDa protein in mature kernels, was shown to have higher mRNA levels in developing endosperm, as compared to inbred lines W23 and W64A. Differences in mRNA levels could not be explained by differences in transcription rate of the 10 kDa zein gene, indicating differential post-transcriptional regulation of this storage protein in the different inbred lines analyzed. Among progeny segregating for the BSSS-53 allele of the 10 kDa zein structural gene Zps10/(22), mRNA levels are independent of Zps10/(22) segregation, indicating that post-transcriptional regulation of mRNA levels takes place via a trans-acting mechanism. In the same progeny, mRNA levels are also independent of allelic segregation of the regulatory locus Zpr10/(22). Thus, the trans-acting factor encoded by Zpr10/(22) determines accumulation of 10 kDa zein at a translational or post-translational step. Multiple trans-acting factors are therefore involved in post-transcriptional regulation of the methionine-rich 10 kDa zein.
1992
Ueda, T, Waverczak W, Ward K, Sher N, Ketudat M, Schmidt RJ, Messing J.  1992.  Mutations of the 22- and 27-kD zein promoters affect transactivation by the Opaque-2 protein. The Plant cell. 4:701-9. AbstractWebsite
By utilizing a homologous transient expression system, we have demonstrated that the Opaque-2 (O2) gene product O2 confers positive trans-regulation on a 22-kD zein promoter. This trans-acting function of the O2 protein is mediated by its sequence-specific binding to a cis element (the O2 target site) present in the 22-kD zein promoter. A multimer of a 32-bp promoter fragment containing this O2 target site confers transactivation by O2. A single nucleotide substitution in the O2 target sequence not only abolishes O2 binding in vitro, but also its response to transactivation by O2 in vivo. We have also demonstrated that an amino acid domain including the contiguous basic region and the heptameric leucine repeat is essential for the trans-acting function of the O2 protein. Similar but not identical O2 target sequence motifs can be found in the promoters of zein genes of different molecular weight classes. Conversion of such a motif in the 27-kD zein promoter to an exact O2 target sequence by site-directed mutagenesis was sufficient to increase the binding affinity of the O2 protein in vitro and to confer transactivation by O2 in vivo.
1993
Schickler, H.  1993.  Repression of the high-methionine zein gene in the maize inbred line Mo17. Plant Journal. 3:221-229..Website
1994
Chaudhuri, S, Messing J.  1994.  Allele-specific parental imprinting of dzr1, a posttranscriptional regulator of zein accumulation. Proceedings of the National Academy of Sciences of the United States of America. 91:4867-71. AbstractWebsite
Parental imprinting describes the phenomenon of unequivalent gene function based on transmission from the female or male parent. We have discovered parental imprinting of an allele of the dzr1 locus that posttranscriptionally regulates the accumulation of 10-kDa zein in the maize endosperm. The imprinted allele of MO17 inbred origin, dzr1 + MO17, conditions low accumulation of the 10-kDa zein and is dominant when transmitted through the female but recessive when transmitted through the male. Analyzing endosperms with equal parental contributions of dzr1 + MO17 ruled out the possibility that the unequivalent phenotype of dzr1 + MO17 was due to parental dosage imbalance in the triploid endosperm. Second-generation studies show that the dominant or recessive phenotype of dzr1 + MO17 is determined at every generation based on immediate parental origin with no grandparental effect.
Das, OP, Messing J.  1994.  Variegated phenotype and developmental methylation changes of a maize allele originating from epimutation. Genetics. 136:1121-41. AbstractWebsite
Two instances of genetic transmission of spontaneous epimutation of the maize P-rr gene were identified. Transmission gave rise to two similar, moderately stable alleles, designated P-pr-1 and P-pr-2, that exhibited Mendelian behavior. Both isolates of P-pr conditioned a variable and variegated phenotype, unlike the uniform pigmentation conditioned by P-rr. Extensive genomic analysis failed to reveal insertions, deletions or restriction site polymorphisms between the new allele and its progenitor. However, methylation of the P gene was increased in P-pr relative to P-rr, and was greatly reduced (though not lost) in a revertant to uniform pigmentation. Variability in pigmentation conditioned by P-pr correlated with variability in transcript levels of the P gene, and both correlated inversely with variability in its methylation. Part of the variability in methylation could be accounted for by a developmental decrease in methylation in all tissues of plants carrying P-pr. We hypothesize that the variegated phenotype results from a general epigenetic pathway which causes a progressive decrease in methylation and increase in expression potential of the P gene as a function of cell divisions in each meristem of the plant. This renders all tissues chimeric for a functional gene; chimerism is visualized as variegation only in pericarp due to the tissue specificity of P gene expression. Therefore, this allele that originates from epimutation may exemplify an epigenetic mechanism for variegation in maize.
1995
Lund, G, Messing J, Viotti A.  1995.  Endosperm-specific demethylation and activation of specific alleles of alpha-tubulin genes of Zea mays L. Molecular & general genetics : MGG. 246:716-22. AbstractWebsite
We have investigated the methylation status of the alpha-tubulin genes, and the degree of accumulation of their mRNAs in endosperm, embryo and seedling tissues of Zea mays L. We have found that many of the alpha-tubulin genes are differentially demethylated in the endosperm relative to the embryo and seedling. However, only for tub alpha 2 and tub alpha 4 could a correlation between DNA demethylation and increased RNA accumulation be detected. By analyzing the inbred lines W64A and A69Y and their reciprocal crosses, we have also identified in the endosperm two alpha-tubulin genes, tub alpha 3 and tub alpha 4, that are differentially demethylated if transmitted by the maternal germline, but that remain hypermethylated when transmitted by the paternal germline.
Lund, G, Prem Das O, Messing J.  1995.  Tissue-specific DNase I-sensitive sites of the maize P gene and their changes upon epimutation. The Plant Journal. 7:797-807.Website
1997
Bradeen, JM, Timmermans MC, Messing J.  1997.  Dynamic genome organization and gene evolution by positive selection in geminivirus (Geminiviridae). Molecular biology and evolution. 14:1114-24. AbstractWebsite
Geminiviruses (Geminiviridae) are a diverse group of plant viruses differing from other known plant viruses in possessing circular, single-stranded DNA. Current classification divides the family into three subgroups, defined in part by genome organization, insect vector, and plant host range. Previous phylogenetic assessments of geminiviruses have used DNA and/or amino acid sequences from the replication-associated and coat protein genes and have relied predominantly on distance analyses. We used amino acid and DNA sequence data from the replication-associated and coat protein genes from 22 geminivirus types in distance and parsimony analyses. Although the results of our analyses largely agree with those reported previously, we could not always predict viral relationships based on genome organization, plant host, or insect vector. Loss of correlation of these traits with phylogeny is likely due to improved sampling of geminivirus types. Unrooted parsimony trees suggest multiple independent origins for the monopartite genome. genome organization is therefore a dynamic character. Estimates of nonsynonymous and synonymous nucleotide substitutions for extant and inferred ancestral sequences were used to evaluate hypotheses that the replication-associated and coat protein sequences evolve to accommodate plant host and insect vector specificities, respectively. Results suggest that plant host specificity does not solely direct replication-associated protein-evolution but that coat protein sequence does evolve in response to insect vector specificity. Genome organization and, possibly, plant host specificity are not reliable taxonomic characters.