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Papers by Thomas Sims

Scientific Reports, 2019

taka-aki tamura 2 & Yuki Yamaguchi 1 transcription and DNA damage repair act in a coordinated man... more taka-aki tamura 2 & Yuki Yamaguchi 1 transcription and DNA damage repair act in a coordinated manner. Recent studies have shown that double-strand DNA breaks (DsBs) are repaired in a transcription-coupled manner. Active transcription results in a faster recruitment of DsB repair factors and expedites DNA repair. on the other hand, transcription is repressed by DNA damage through multiple mechanisms. We previously reported that tLp, a tAtA box-binding protein (tBp) family member that functions as a transcriptional regulator, is also involved in DNA damage-induced apoptosis. However, the mechanism by which TLP affects DNA damage response was largely unknown. Here we show that tLp-mediated global transcriptional repression after DsBs is crucial for apoptosis induction by DNA-damaging agents such as etoposide and doxorubicin. Compared to control cells, tLp-knockdown cells were resistant to etoposideinduced apoptosis and exhibited an elevated level of global transcription after etoposide exposure. DSBs were efficiently removed in transcriptionally hyperactive TLP-knockdown cells. However, forced transcriptional shutdown using transcriptional inhibitors α-amanitin and 5,6-dichloro-1-ß-Dribofuranosylbenzimidazole (DRB) slowed down DsB repair and resensitized tLp-knockdown cells to etoposide. taken together, these results indicate that tLp is a critical determinant as to how cells respond to DsBs and triggers apoptosis to cells that have sustained DNA damage. It has been reported that transcription and DNA damage repair act in a coordinated manner. Active transcription accelerates DNA damage repair through multiple mechanisms. In transcription-coupled nucleotide excision repair, bulky base adducts, such as pyrimidine dimers, induced by UV light or environmental mutagens are removed preferentially in actively transcribed genes 1. Moreover, recent studies revealed that DSBs are also removed more efficiently in actively transcribed genes 2-5. Transcriptionally engaged RNA polymerase II (RNAPII) recruits factors involved in homologous recombination (HR) repair to damaged sites 2. Furthermore, it is demonstrated that nascent RNA is used as a template for HR repair 4,5. Thus, transcription plays an important role in the repair of damaged DNA. On the other hand, DNA damage globally represses transcriptional activity by multiple pathways 6-9. Shanbhag et al. showed that ATM-dependent ubiquitination of histone H2A-K119 results in the prevention of RNAPII elongation at DSB sites 6. Kakarougkas et al. showed that the chromatin remodeling complex PBAF is important for DSB-induced transcriptional repression 8. However, the molecular mechanism underlying DNA damage-induced transcriptional repression is not fully understood. Regardless, it is speculated that global transcriptional repression facilitates DNA repair by eliminating RNAPII, which could interfere with DNA repair, from damaged DNA 6,8,9. The anti-cancer drug etoposide is a DNA topoisomerase II (Topo II) inhibitor that induces DSBs 10,11. Topo II catalyzes a two-step reaction involving DNA scission. A covalent link between Topo II and cleaved DNA is

Recent Research Developments in Plant Molecular Biology, 2005

Plant molecular biology, 2001

To investigate protein-protein interactions in gametophytic self-incompatibility, we used a yeast... more To investigate protein-protein interactions in gametophytic self-incompatibility, we used a yeast two-hybrid assay to identify proteins that could interact with the S-ribonuclease protein. These assays identified a pollen-expressed protein, which we have named PhSBP1, that appears to bind with a high degree of specificity to the Petunia hybrida S-ribonuclease. Although PhSBP1 activates reporter gene expression only when expressed in tandem with a S-RNAse bait protein, binding is not allele-specific. Sequence analysis demonstrated that PhSBP1 contained a C-terminal cysteine-rich region that includes a RING-HC domain. Because many RING-finger domain proteins appear to function as E3 ubiquitin ligases, our results suggest that ubiquitination and protein degradation may play a role in regulating self-incompatibility interactions. Together, these results suggest that PhSBPI may be a candidate for the recently proposed general inhibitor (RI) of self-incompatibility ribonucleases.

The Journal of biological chemistry, Jan 25, 1981

Polyadenylated RNA has been isolated from maize leaves at various times during greening of etiola... more Polyadenylated RNA has been isolated from maize leaves at various times during greening of etiolated seedlings and used to prime the wheat germ cell-free translation system. Levels of translatable messenger RNA for phosphoenolpyruvate carboxylase increase with the length of the illumination period. The pattern of the increase in translatable mRNA for the enzyme is similar to that of the increase in phosphoenolpyruvate carboxylase protein previously observed in intact tissues. Phosphoenolpyruvate carboxylase synthesized in vivo migrates as a doublet band on gradient sodium dodecyl sulfate-polyacrylamide gels. A similar doublet has been seen occasionally with the products of cell-free translation.

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Page 1. 10 Protein Interactions in S-RNase-Based Gametophytic Self-Incompatibility Thomas L. Sims... more Page 1. 10 Protein Interactions in S-RNase-Based Gametophytic Self-Incompatibility Thomas L. Sims Department of Biological Sciences, Northern Illinois University USA 1. Introduction With well over 200,000 documented species ...

PLANT PHYSIOLOGY, 1994

To determine the ability of isolated S-locus promoter sequences to direct organ-specific gene exp... more To determine the ability of isolated S-locus promoter sequences to direct organ-specific gene expression, we used microprojectile bombardment to introduce chimeric S-allele/beta-glucuronidase genes into different tissues of Petunia hybrida for transient expression. Histochemical staining showed that S-locus/beta-glucuronidase fusions were expressed in pistil, ovary, and petal tissue. No expression of the chimeric genes was detected in leaves or in mature pollen, either by histochemical staining or by fluorescence assays. RNA blot hybridization confirmed that low levels of S-locus mRNA accumulate in petals and ovaries in vivo. Analysis of the expression pattern of S-locus promoter deletions showed that sequences in the immediate vicinity of the TATA box were sufficient to confer qualitatively correct organ-specific expression of beta-glucuronidase. To further investigate the potential for S-ribonuclease expression in pollen, we used the polymerase chain reaction to amplify RNA accumulated in developing anthers. These assays demonstrated that mRNA for the S-ribonuclease accumulates to low levels in developing anthers several days prior to corolla opening and pollen anthesis. We discuss these results in light of current models of self-incompatibility.

PLANT PHYSIOLOGY, 1980

Illumination (22,000 lumens per meter(2)) of etiolated maize plants for 80 hours brings about a 5... more Illumination (22,000 lumens per meter(2)) of etiolated maize plants for 80 hours brings about a 5-fold increase in phosphoenolpyruvate carboxylase activity per unit of protein. An increase in carboxylase protein and incorporation of [(35)S]methionine into the protein occurs simultaneously with the activity increase. In green plants, the level of phosphoenolpyruvate carboxylase protein and enzyme activity is dependent on the intensity of light during growth. These results are consistent with the conclusion that the activity increase results from light-stimulated de novo synthesis of phosphoenolypyruvate carboxylase protein.

Critical Reviews in Plant Sciences, 1993

Page 1. Critical Reviews in Plant Sciences, 12(1/2):129-167 (1993) Genetic Regulation of Self-Inc... more Page 1. Critical Reviews in Plant Sciences, 12(1/2):129-167 (1993) Genetic Regulation of Self-Incompatibility Thomas L. Sims Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115 ABSTRACT: Self-incompatibility ...

CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 2007

Gametophytic self-incompatibility (GSI), a genetic mechanism that acts to prevent self-fertilizat... more Gametophytic self-incompatibility (GSI), a genetic mechanism that acts to prevent self-fertilization in many angiosperms, is based on the ability of the pistil to selectively inhibit growth of self pollen while allowing the growth of non-self pollen. In the most widespread variant of GSI (studied most thoroughly in the Solanaceae, Rosaceae and Plantaginaceae), a style-expressed ribonuclease (the S-RNase) is imported into

Petunia hybrida, the garden petunia, has been used as a model system for decades for evolutionary... more Petunia hybrida, the garden petunia, has been used as a model system for decades for evolutionary, developmental and physiological genetics. It is also, at least in the USA, the most popular ornamental plant in overall sales. Nevertheless, Petunia hybrida is essentially an “artificial” species resulting from crossing two progenitor species, the white-flowered, generally self-compatible Petunia axillaris and the red-flowered, self-incompatible Petunia integrifolia. The international consortium of petunia researchers, The Petunia Platform, has initiated a project to sequence, assemble and annotate the genomes of Petunia integrifolia (subsp. inflata) and Petunia axillaris. Both genomes have been sequenced using Illumina paired-end reads to a depth of 65-70X, with an estimated genome size of 1.2 Gbp. A preliminary assembly of P. inflata has been carried out using SOAPdenovo, with annotation being carried out using MAKER. Assembly of P. axillaris is in progress. We will report our progre...

Petunia, 2009

Gametophytic self-incompatibility (GSI), which prevents growth of a pollen tube through the style... more Gametophytic self-incompatibility (GSI), which prevents growth of a pollen tube through the style, provides a means of preventing self-pollination. Seen in most eudicot plant families, GSI in the genus Petunia was described by Darwin in the 19th century. By the time the first edition of this monograph was published in 1984, nearly a century later, most of the readily observable phenomena associated with self-incompatibility in the genus Petunia had been described and, as in a number of other plant systems, it had been demonstrated to depend on the actions of genes encoded at a single highly polymorphic S-locus. Molecular research of the past two decades has provided a depth of understanding into the mechanisms underlying the earlier observations, particularly in the identification of a number of SIassociated genes, their sites of action, and to some extent the mechanisms involved. This chapter summarizes what has been learned, with a focus on the molecular biology underlying GSI in Petunia, and highlights the major questions that remain unanswered.

The Plant Cell, 1989

We characterized the structure, organization, and expression of genes that encode the soybean gly... more We characterized the structure, organization, and expression of genes that encode the soybean glycinins, a family of storage proteins synthesized exclusively in seeds during embryogenesis. Five genes encode the predominant glycinin subunits found in soybeans, and they have each been cloned, sequenced, and compared. The five genes have diverged into two subfamilies that are designated as Group-I and Group-II glycinin genes. Each glycinin gene contains four exons and three introns like genes that encode related proteins in other legumes. Two other genes have been identified and designated as "glycinin-related" because they hybridize weakly with the five glycinin genes.

THE PLANT CELL ONLINE, 1990

We investigated the structure and expression of three S-alleles of Petunia hybrida in self-incomp... more We investigated the structure and expression of three S-alleles of Petunia hybrida in self-incompatible varieties and in a pseudo-self-compatible line in which the self-incompatibility response is defective. Comparison of derived amino acid sequences from different gametophytic S-alleles revealed a pattern of sequence conservation and variability that was highly nonrandom. In self-incompatible varieties, petunia S-locus mRNA accumulates preferentially in styles during the transition from bud self-compatibility to self-incompatibility. S-Allele sequences homologous to the cloned S, allele were present in a pseudo-self-compatible variety, and were expressed at levels indistinguishable from those observed in a self-incompatible line homozygous for the SI allele. Taken together, our data indicate that (1) limited sequence differences may confer allelic specificity, (2) S-locus mRNAs accumulate in a precise organ-specific pattern during floral development, and (3) the ability to inhibit the growth of incompatible pollen tubes appears to require a threshold accumulation of the stylar gene product, along with the participation of as yet undefined pollen gene products.

Nucleic Acids Research, 1989

Biochemical Society Transactions, 2010

The recent identification of several proteins playing key roles in S-RNase-based gametophytic sel... more The recent identification of several proteins playing key roles in S-RNase-based gametophytic self-incompatibility has led both to a greater understanding of the molecular biology of this response, as well as to questions regarding the precise mechanism by which compatible pollen tubes are recognized and accepted. A proposed variant SCF(SLF) (where SCF is SSK1/cullin/F-box and SLF is S-locus F-box) ubiquitin ligase complex is thought to play a central role in recognizing and inhibiting non-self S-RNases, but the exact role of ubiquitination remains unclear. How the possible sequestration of non-self S-RNases in a pollen vacuolar compartment can be reconciled with the need for protein interaction between S-RNase and the SCF(SLF) complex needs to be determined. Current work to answer these questions focuses on more precisely defining quantitative protein interactions and subcellular localization of proteins involved in S-RNase-based gametophytic self-incompatibility.

Surgery, 2011

Background-High-grade glioblastomas have immature, leaky tumor blood vessels that impede the effi... more Background-High-grade glioblastomas have immature, leaky tumor blood vessels that impede the efficacy of adjuvant therapy. We assessed the ability of human interferon-beta (hIFN-β) delivered locally via gene transfer to effect vascular stabilization in an orthotopic glioblastoma xenograft resection model.

Sex Plant Reprod, 2001

Neil O. Anderson Peter D. Ascher Beata Barnabas Spencer CH Barrett Dmitry A. Belostotsky Anuj Bha... more Neil O. Anderson Peter D. Ascher Beata Barnabas Spencer CH Barrett Dmitry A. Belostotsky Anuj Bhatt Ross A. Bicknell James H. Birchler Roy C. Brown Jean-Philippe Vielle Calzada David D. Cass Maria Charzinska Anne Marie Chevre Mark Cock Lucia Colombo Mauro Cresti Darleen DeMason Jan Derksen Hugh G. Dickinson Peter van Dijk ... Peter Dodds Jaroslav Dolezel Thomas Dresselhaus Christian Dumas Jean-Emanuel Faure Jose A. Feijo Veronica E. Franklin-Tong Thierry Gaude Robert B. Goldberg Inna Golubovskaya Carl D. Grant Douglas Hamilton ...