Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

Twin-ribozyme introns contain a branching ribozyme (GIR1) followed by a homing endonuclease (HE) encoding sequence embedded in a peripheral domain of a group I splicing ribozyme (GIR2). GIR1 catalyses the formation of a lariat with 3 nt in the loop, which caps the HE mRNA. GIR1 is structurally related to group I ribozymes raising the question about how two closely related ribozymes can carry out very different reactions. Modelling of GIR1 based on new biochemical and mutational data shows an extended substrate domain containing a GoU pair distinct from the nucleophilic residue that dock onto a catalytic core showing a different topology from that of group I ribozymes. The differences include a core J8/7 region that has been reduced and is complemented by residues from the pre-lariat fold. These findings provide the basis for an evolutionary mechanism that accounts for the change from group I splicing ribozyme to the branching GIR1 architecture. Such an evolutionary mechanism can be applied to other large RNAs such as the ribonuclease P

Molecular characterization and genetic mapping of DNA sequences encoding the Type I chlorophyll a/b-binding polypeptide of photosystem I in Lycopersicon esculentum (tomato)

We report the isolation and characterization of a tomato nuclear gene encoding a chlorophyll a/b-binding (CAB) protein of photosystem I (PSI). The coding nucleotide sequence of the gene, designated Cab -6B, is different at eight positions from that of a previously isolated cDNA clone derived from the Cab -6A gene, but the two genes encode identical proteins. Sequence comparison with the cDNA clone revealed the presence of three short introns in Cab -6B. Genetic mapping experiments demonstrate that Cab -6A and Cab -6B are tightly linked and reside on chromosome 5, but the physical distance between the two genes is at least 7 kilobases. Cab -6A and Cab -6B have been designated Type I PSI CAB genes. They are the only two genes of this branch of the CAB gene family in the tomato genome, and they show substantial divergence to the genes encoding CAB polypeptides of photosystem II. The Type I PSI CAB genes, like the genes encoding PSII CAB proteins, are highly expressed in illuminated leaf tissue and to a lesser extent in other green organs.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43459/1/11103_2004_Article_BF00166457.pd

The tomato Cab -4 and Cab -5 genes encode a second type of CAB polypeptides localized in Photosystem II

The photosynthetic apparatus of plant chloroplasts contains two photosystems, termed Photosystem I (PSI) and Photosystem II (PSII). Both PSI and PSII contain several types of chlorophyll a/b-binding (CAB) polypeptides, at least some of which are structurally related. It has been previously shown that multiple genes encoding one type of PSII CAB polypeptides exist in the genome of many higher plants. In tomato, there are at least eight such genes, distributed in three independent loci. Genes encoding a second type of CAB polypeptides have been isolated from several plant species, but the precise location of the gene products has not been determined. Here we show that tomato has two unlinked genes encoding this second type and that this type of CAB polypeptide is also localized in PSII.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43458/1/11103_2004_Article_BF00015643.pd

A new member of the CAB gene family: structure, expression and chromosomal location of Cab -8, the tomato gene encoding the Type III chlorophyll a/b-binding polypeptide of photosystem I

We have previously reported the isolation and characterization of tomato nuclear genes encoding two types of chlorophyll a/b-binding (CAB) polypeptides localized in photosystem (PS) I and two types of CAB polypeptides localized in PSII. Sequence comparisons shows that all these genes are related to each other and thus belong to a single gene family. Here we report the isolation and characterization of an additional member of the tomato CAB gene family, the single tomato nuclear gene, designated Cab -8, which encodes a third type of CAB polypeptide localized in PSI. The protein encoded by Cab -8 is 65% and 60% divergent from the PSI Type I and Type II CAB polypeptides, respectively. The latter two are 65% divergent from each other. Only some short regions of the polypeptides are strongly conserved. The Cab -8 locus maps to chromosome 10, 9 map units from Cab -7, the gene encoding the Type II PSI CAB polypeptide. The Cab -8 gene contains two introns; the first intron matches in position the single intron in the Type II PSII CAB genes and the second intron matches in position the second intron in the Type II PSI CAB gene. Like other CAB genes, Cab -8 is light-regulated and is highly expressed in the leaf and to a lesser extent in other green organs.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43422/1/11103_2004_Article_BF00043203.pd

Systems biology discoveries using non-human primate pluripotent stem and germ cells: novel gene and genomic imprinting interactions as well as unique expression patterns

The study of pluripotent stem cells has generated much interest in both biology and medicine. Understanding the fundamentals of biological decisions, including what permits a cell to maintain pluripotency, that is, its ability to self-renew and thereby remain immortal, or to differentiate into multiple types of cells, is of profound importance. For clinical applications, pluripotent cells, including both embryonic stem cells and adult stem cells, have been proposed for cell replacement therapy for a number of human diseases and disorders, including Alzheimer's, Parkinson's, spinal cord injury and diabetes. One challenge in their usage for such therapies is understanding the mechanisms that allow the maintenance of pluripotency and controlling the specific differentiation into required functional target cells. Because of regulatory restrictions and biological feasibilities, there are many crucial investigations that are just impossible to perform using pluripotent stem cells (PSCs) from humans (for example, direct comparisons among panels of inbred embryonic stem cells from prime embryos obtained from pedigreed and fertile donors; genomic analysis of parent versus progeny PSCs and their identical differentiated tissues; intraspecific chimera analyses for pluripotency testing; and so on). However, PSCs from nonhuman primates are being investigated to bridge these knowledge gaps between discoveries in mice and vital information necessary for appropriate clinical evaluations. In this review, we consider the mRNAs and novel genes with unique expression and imprinting patterns that were discovered using systems biology approaches with primate pluripotent stem and germ cells

Isolation and sequence of a tomato cDNA clone encoding subunit II of the photosystem I reaction center

We report here the isolation and nucleotide sequence of a cDNA clone encoding a phtosystem I polypeptide that is recognized by a polyclonal antibody prepared against subunit II of the photosystem I reaction center. The transit peptide processing site was determined to occur after Met 50 by N terminal sequencing. The decuced sequence of this protein predicts that the polypeptide has a net positive charge (pI=9.6) and no membrane spanning regions are evident from the hydropathy plot. Based on these considerations and the fact that subunit II is solubilized by alkali treatment of thylakoids, we concluded that subunit II is an extrinsic membrane protein. The absence of hydrophobic regions characteristic of thylakoid transfer domains furthermore implies that subunit II is localized on the stromal side of the membrane.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43419/1/11103_2004_Article_BF00014949.pd

Chlorophyll a/b binding (CAB) polypeptides of CP29, the internal chlorophyll a/b complex of PSII: characterization of the tomato gene encoding the 26 kDa (type 1) polypeptide, and evidence for a second CP29 polypeptide

CP29, the core chlorophyll a/b (CAB) antenna complex of Photosystem II (PSII), has two nuclearencoded polypeptides of approximately 26 and 28 kDa in tomato ( Lycopersicon esculentum ). Cab9, the gene for the Type 1 (26 kDa) CP29 polypeptide was cloned by immunoscreening a tomato leaf cDNA library. Its identity was confirmed by sequencing tryptic peptides from the mature protein. Cab9 is a single-copy gene with five introns, the highest number found in a CAB protein. In vitro transcription-translation gave a 31 kDa precursor which was cleaved to about 26 kDa after import into isolated tomato chloroplasts. The Cab9 polypeptide has the two highly conserved regions common to all CAB polypeptides, which define the members of this extended gene family. Outside of the conserved regions, it is only slightly more closely related to other PSII CABs than to PSI CABs. Sequence analysis of tryptic peptides from the Type II (28 kDa) CP29 polypeptide showed that it is also a member of the CAB family and is very similar or identical to the CP29 polypeptide previously isolated from spinach. All members of the CAB family have absolutely conserved His, Gln and Asn residues which could ligate the Mg atoms of the chlorophylls, and a number of conserved Asp, Glu, Lys and Arg residues which could form H-bonds to the polar groups on the porphyrin rings. The two conserved regions comprise the first and third predicted trans-membrane helices and the stroma-exposed segments preceding them.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47577/1/438_2004_Article_BF00259681.pd

Aerosol-assisted route to low-E transparent conductive gallium-doped zinc oxide coatings from pre-organized and halogen-free precursor

Thermal control in low-emission windows is achieved by the application of glazings, which are simultaneously optically transparent in the visible and reflective in the near-infrared (IR). This phenomenon is characteristic of coatings with wide optical band gaps that have high enough charge carrier concentrations for the material to interact with electromagnetic radiation in the IR region. While conventional low-E coatings are composed of sandwiched structures of oxides and thin Ag films or of fluorinated SnO2 coatings, ZnO-based glazing offers an environmentally stable and economical alternative with competitive optoelectronic properties. In this work, gallium-doped zinc oxide (GZO) coatings with properties for low-E coatings that exceed industrial standards (Tvisible > 82%; R2500 nm > 90%; λ(plasma) = 1290 nm; ρ = 4.7 × 10−4 Ω cm; Rsh = 9.4 Ω·□−1) are deposited through a sustainable and environmentally friendly halogen-free deposition route from [Ga(acac)3] and a pre-organized zinc oxide precursor [EtZnOiPr]4 (1) via single-pot aerosol-assisted chemical vapor deposition. GZO films are highly (002)-textured, smooth and compact without need of epitaxial growth. The method herein describes the synthesis of coatings with opto-electronic properties commonly achievable only through high-vacuum methods, and provides an alternative to the use of pyrophoric ZnEt2 and halogenated SnO2 coatings currently used in low-emission glazing and photovoltaic technology