Biomedical subjects

Eric P Beers

Publications and source records attributed to Eric P Beers.

4 recordsLinked to original sources

PubMed2006

Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana.

Our knowledge of the genetic control of wood formation (i.e., secondary growth) is limited. Here, we present a novel approach to unraveling the gene network regulating secondary xylem development in Arabidopsis, which incorporates complementary platforms of comparative-transcriptome analyses such as "digital northern" and "digital in situ" analysis. This approach effectively eliminated any genes that are expressed in either non-stem tissues/organs ("digital northern") or phloem and non-vascular regions ("digital in situ"), thereby identifying 52 genes that are upregulated only in the xylem cells of secondary growth tissues as "core xylem gene set". The proteins encoded by this gene set participate in signal transduction, transcriptional regulation, cell wall metabolism, and unknown functions. Five of the seven signal transduction-related genes represented in the core xylem gene set encode the essential components of ROP (Rho-related GTPase from plants) signaling cascade. Furthermore, the analysis of promoter sequences of the core xylem gene set identified a novel cis-regulatory element, ACAAAGAA. The functional significances of this gene set were verified by several independent experimental and bioinformatics methods.

Arabidopsis↗

PubMed2005

The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl.

The growth of secondary xylem and phloem depends on the division of cells in the vascular cambium and results in an increase in the diameter of the root and stem. Very little is known about the genetic mechanisms that control cambial activity and the differentiation of secondary xylem and phloem cell types. To begin to identify new genes required for vascular cell differentiation and function, we performed genome-wide expression profiling of xylem and phloem-cambium isolated from the root-hypocotyl of Arabidopsis (Arabidopsis thaliana). Gene expression in the remaining nonvascular tissue was also profiled. From these transcript profiles, we assembled three sets of genes with expression significantly biased toward xylem, phloem-cambium, or nonvascular tissue. We also assembled three two-tissue sets of genes with expression significantly biased toward xylem/phloem-cambium, xylem/nonvascular, or phloem-cambium/nonvascular tissues. Localizations predicted by transcript profiles were supported by results from promoter-reporter and reverse transcription-polymerase chain reaction experiments with nine xylem- or phloem-cambium-biased genes. An analysis of the members of the phloem-cambium gene set suggested that some genes involved in regulating primary meristems are also regulators of the cambium. Secondary phloem was implicated in the synthesis of auxin, glucosinolates, cytokinin, and gibberellic acid. Transcript profiles also supported the importance of class III HD ZIP and KANADI transcription factors as regulators of radial patterning during secondary growth, and identified several members of the G2-like, NAC, AP2, MADS, and MYB transcription factor families that may play roles as regulators of xylem or phloem cell differentiation and activity.

Arabidopsis↗

PubMed2004

The S8 serine, C1A cysteine and A1 aspartic protease families in Arabidopsis.

The Arabidopsis thaliana genome has over 550 protease sequences representing all five catalytic types: serine, cysteine, aspartic acid, metallo and threonine (MEROPS peptidase database, http://merops.sanger.ac.uk/), which probably reflect a wide variety of as yet unidentified functions performed by plant proteases. Recent indications that the 26S proteasome, a T1 family-threonine protease, is a regulator of light and hormone responsive signal transduction highlight the potential of proteases to participate in many aspects of plant growth and development. Recent discoveries that proteases are required for stomatal distribution, embryo development and disease resistance point to wider roles for four additional multigene families that include some of the most frequently studied (yet poorly understood) plant proteases: the subtilisin-like, serine proteases (family S8), the papain-like, cysteine proteases (family C1A), the pepsin-like, aspartic proteases (family A1) and the plant matrixin, metalloproteases (family M10A). In this report, 54 subtilisin-like, 30 papain-like and 59 pepsin-like proteases from Arabidopsis, are compared with S8, C1A and A1 proteases known from other plant species at the functional, phylogenetic and gene structure levels. Examples of structural conservation between S8, C1A and A1 genes from rice, barley, tomato and soybean and those from Arabidopsis are noted, indicating that some common, essential plant protease roles were established before the divergence of monocots and eudicots. Numerous examples of tandem duplications of protease genes and evidence for a variety of restricted expression patterns suggest that a high degree of specialization exists among proteases within each family. We propose that comprehensive analysis of the functions of these genes in Arabidopsis will firmly establish serine, cysteine and aspartic proteases as regulators and effectors of a wide range of plant processes.

Amino Acid Sequence↗

PubMed2002

The Arabidopsis xylem peptidase XCP1 is a tracheary element vacuolar protein that may be a papain ortholog.

XCP1 is a xylem-specific papain-like cysteine peptidase in Arabidopsis. To determine whether XCP1 could be involved in tracheary element autolysis, promoter activity and localization of XCP1 were investigated using XCP1 promoter-beta-glucuronidase fusions and immunofluorescence confocal microscopy. A tracheary element expression pattern was detected for XCP1. Results from confocal microscopy and biochemical subcellular fractionation indicated that XCP1 was localized in the vacuole. Ectopic expression of XCP1 resulted in a reduction in plant size in some lines and early leaf senescence, as indicated by early loss of leaf chlorophyll. Reduced plant size was correlated with higher levels of XCP1, as shown by immunoblot and peptidase activity gel analyses. The XCP1 prodomain exhibits exceptionally high similarity (greater than 80%) to the prodomains of papain and other papain-like enzymes isolated from papaya (Carica papaya) laticifers when compared with all other reported papain-like enzymes. The potential for XCP1 and papain to perform common functions as catalysts of autolytic processing following cell death due to programmed suicide or to wounding is discussed.

Arabidopsis↗