Biomedical subjects

Bo Segerman

Publications and source records attributed to Bo Segerman.

6 recordsLinked to original sources

PubMed2006

Poplar carbohydrate-active enzymes. Gene identification and expression analyses.

Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr. & Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar (Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis (Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.

Arabidopsis↗

PubMed2006

Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis.

Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) x tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5'-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.

Cell Wall↗

PubMed2005

A genomic approach to investigate developmental cell death in woody tissues of Populus trees.

BACKGROUND: Poplar (Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag (EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. RESULTS: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. CONCLUSIONS: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.

Apoptosis Regulatory Proteins↗

PubMed2004

A Populus EST resource for plant functional genomics.

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

Ecosystem↗

PubMed2003

Molecular dissection of GTP exchange and hydrolysis within the ternary complex of tubulin heterodimers and Op18/stathmin family members.

The ubiquitous Op18 and the neural RB3 and SCG10 proteins are members of the oncoprotein18/stathmin family of microtubule regulators. These proteins bind two tubulin heterodimers via two imperfect helical repeats to form a complex of heterodimers aligned head-to-tail. Here we have analyzed GTP exchange and GTP hydrolysis at the exchangeable GTP-binding site (E-site) of tubulin heterodimers in complex with Op18, RB3, or SCG10. These proteins stimulate a low and indistinguishable rate of GTP hydrolysis, and our results show that GTP exchange is blocked at both E-sites of the ternary complex, whereas GTP hydrolysis only occurs at one of the two E-sites. Results from mutational analysis of clusters of hydrophobic residues within the first helical repeat of Op18 suggest that GTP is hydrolyzed at the E-site that is interfaced between the head-to-tail arranged heterodimers, which is consistent with predicted GTPase productive interactions between the two tubulin heterodimers. Our mutational analysis has also indicated that Op18/stathmin family members actively restrain the otherwise potent GTPase productive interactions that are generated by longitudinal interactions within protofilaments. We conclude that tubulin heterodimers in complex with Op18/stathmin family members are subject to allosteric effects that prevent futile cycles of GTP hydrolysis.

Allosteric Regulation↗

PubMed2003

Autonomous and phosphorylation-responsive microtubule-regulating activities of the N-terminus of Op18/stathmin.

Op18 is the prototypical member of a family of phosphorylation-responsive regulators of microtubule (MT) dynamics. Previous dissection of Op18 has suggested that it has a functional dichotomy in which an intact N-terminus is required for catastrophe promotion (i.e. transition from growing to shrinking MTs), whereas an intact C-terminus is required for efficient ternary Op18-tubulin complex formation and the resultant tubulin-sequestering activity. Here we have expressed and functionally analyzed the properties of the N-terminus of Op18. The data show that the N-terminal 57 residues are sufficient for low-affinity tubulin interactions, as shown by inhibition of basal GTP hydrolysis of soluble heterodimers. In addition, high concentrations of the Op18 N-terminal portion increased the catastrophe rate during MT assembly in vitro. Overexpression of the N-terminus in a human cell line results in MT destabilization in interphase and phosphorylation-modulated accumulation of metaphase-arrested cells with dense short MTs. These results demonstrate that the N-terminus of Op18 has autonomous activity. Evidently, this activity is enhanced by the increase in tubulin affinity that is provided by the extended alpha-helical portion of native Op18.

Amino Acid Sequence↗