Actin-related proteins are ubiquitous components of chromatin remodelers and are conserved from yeast to man. We have examined the role of the budding yeast actin-related protein Arp6 in gene expression, both as a component of the SWR1 complex (SWR-C) and in its absence. We mapped Arp6 binding sites along four yeast chromosomes using chromatin immunoprecipitation from wild-type and swr1 deleted (swr1Delta) cells. We find that a majority of Arp6 binding sites coincide with binding sites of Swr1, the catalytic subunit of SWR-C, and with the histone H2A variant Htz1 (H2A.Z) deposited by SWR-C. However, Arp6 binding detected at centromeres, the promoters of ribosomal protein (RP) genes, and some telomeres is independent of Swr1 and Htz1 deposition. Given that RP genes and telomeres both show association with the nuclear periphery, we monitored the ability of Arp6 to mediate the localization of chromatin to nuclear pores. Arp6 binding is sufficient to shift a randomly positioned locus to nuclear periphery, even in a swr1Delta strain. Arp6 is also necessary for the pore association of its targeted RP promoters possibly through cell cycle-dependent factors. Loss of Arp6, but not Htz1, leads to an up-regulation of these RP genes. In contrast, the pore-association of GAL1 correlates with Htz1 deposition, and loss of Arp6 reduces both GAL1 activation and peripheral localization. We conclude that Arp6 functions both together with the nucleosome remodeler Swr1 and also without it, to mediate Htz1-dependent and Htz1-independent binding of chromatin domains to nuclear pores. This association is shown to have modulating effects on gene expression.

The protein composition of the venoms of the West African Gaboon viper (Bitis gabonica rhinoceros), the rhinoceros viper (Bitis nasicornis), and the horned puff adder (Bitis caudalis) were analyzed by RP-HPLC, N-terminal sequencing, SDS-PAGE, MALDI-TOF peptide mass fingerprinting, and CID-MS/MS. In line with previous proteomic and transcriptomic analyses showing that snake venom proteins belong to only a few major protein families, the venom proteomes of Bitis gabonica rhinoceros, Bitis nasicornis, and Bitis caudalis comprise, respectively, toxins from 11, 9, and 8 toxin families. Dimeric disintegrins, PLA2 molecules, serine proteinases, a CRISP, C-type lectin-like proteins, L-amino acid oxidases, and snake venom metalloproteases are present in the three Bitis snake venoms, though they depart from each other in the composition and the relative abundance of their toxins. The venom composition appears to keep information on the evolutionary history of congeneric taxa. Protein similarity coefficients used to estimate the similarity of venom proteins of the Bitis taxa sampled here and in previous studies (eg. Bitis arietans and Bitis gabonica gabonica) support the monophyly of the three West African taxa (B.g. gabonica, B.g. rhinoceros, and B. nasicornis) based on genetic distance reconstructions, the lack of alliances between B. arietans and any other Bitis species, and are consistent with the taxonomic association of Bitis caudalis within the differentiated group of small Bitis species. The low level of venom toxin composition similarity between the two conventionally recognized subspecies of Bitis gabonica, B. g. gabonica and B. g. rhinoceros, supports the consideration by some authors of B. g. rhinoceros as a separate species, Bitis rhinoceros. Moreover, our proteomic data fit better to a weighted phylogram based on overall genetic distances than to an unweighted maximum-parsimony tree.

The protein composition of the venoms of the three subspecies of Sistrurus catenatus (S. c. catenatus, tergeminus, and edwardsii) and a basal species, Sistrurus miliarius barbouri, were analyzed by RP-HPLC, N-terminal sequencing, MALDI-TOF peptide mass fingerprinting, and CID-MS/MS. The venoms of the four Sistrurus taxa contain proteins from 11 families. The protein family profile and the relative abundance of each protein group in the different venoms are not conserved. Myotoxins and 2-chain PLA2s were detected only in S.c. catenatus and S.c. tergeminus, whereas C-type BPP and Kunitz-type inhibitors were exclusively found in S.c. edwardsii and Sistrurus miliarius barbouri. Among major protein families, taxa were most similar in their metalloproteases (protein similarity coefficient value: 34%) and most divergent in PLA2s (12%), with values for disintegrins and serine proteases lying between these extremes (25 and 20%, respectively). The patterns of venom diversity points to either a gain in complexity in S. catenatus taxa or a loss of venom diversity occurring early on in the evolution of the group involving the lineage connecting S. milarius to the other taxa. The high degree of differentiation in the venom proteome among recently evolved congeneric taxa emphasizes the uniqueness of the venom composition of even closely related species that have different diets. Comparative proteomic analysis of Sistrurus venoms provides a comprehensive catalog of secreted proteins, which may contribute to a deeper understanding of the biology and ecology of these North American snakes and may also serve as a starting point for studying structure-function correlations of individual toxins.

OBJECTIVE

To investigate the mechanism by which polyethylene glycol (PEG) conjugation (PEGylation) prevents the acylation of octreotide by poly(d,l-lactide-co-glycolide) (PLGA).

METHODS

Octreotide was chemically modified by reaction with succinimidyl propionate-monomethoxy PEG. Each PEGylated octreotide species with different PEG number and modified position was separated by reversed-phase high-performance liquid chromatography (RP-HPLC) and characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with endoproteinase Lys-C digestion. Acylation of octreotide and PEGylated octreotides was observed with hydrophobic and hydrophilic PLGA.

RESULTS

Two mono- and one di-PEGylated octreotides were separated by RP-HPLC. MALDI-TOF MS of the PEGylated products after Lys-C digestion at different pH revealed that the two mono-PEGylated octreotides were modified at the N-terminus and Lys(5) residue, respectively. The interaction of octreotide with PLGA involved an initial adsorption followed by acylation and the subsequent release of octreotide and acylated octreotide. The initial adsorption of octreotide was dependent on the acidity of PLGA. PEGylation of octreotide significantly inhibited the initial adsorption and acylation by PLGA. In particular, the acylation could be completely prevented by mono-PEGylation at the N-terminus of octreotide.

CONCLUSIONS

This study shows that the N-terminus of octreotide is the preferred PEGylation site to prevent acylation in degrading PLGA microspheres. The mono-N-terminally PEGylated octreotide may possibly serve as a new source for somatostatin microsphere formulation.

A unique, late-eluting "basic peak" (relative to the "main peak") was observed by weak cation exchange-HPLC (WCX) for a recombinant monoclonal antibody (mAb) sample. Peak fractions were collected, desalted, and analyzed by high-resolution MS using a top-down characterization approach that provided accurate masses of intact mAb charge isoforms and a comprehensive profile of the structural heterogeneity. The individual light (L) and heavy (H) chain subunits from the main and basic peaks were analyzed by reversed-phase (RP) HPLC/MS after disulfide bond reduction and cysteine alkylation. Three mAb isoforms were detected, and their modifications were localized to H chain. Bottom-up characterization using RP-HPLC/MS peptide mapping and accurate mass measurements identified three distinct H chain C-terminal peptides ending in glycine, lysine, or alpha-amidated proline. The combined analyses showed that the main WCX peak mAb isoform contained two unmodified L chains and two H chains terminating in glycine. Each mAb isoform that coeluted in the basic peak consisted of two unmodified L chain subunits and a single H chain ending in glycine, but the second H chain terminated in lysine for one isoform and alpha-amidated proline for another isoform. The WCX elution positions of the isoforms were consistent with their respective net charge. To the best of our knowledge, the occurrence of C-terminal alpha-amidation in mAbs has not been reported previously.

BACKGROUND

Usher syndrome (USH) is a heterogeneous group of inherited retinitis pigmentosa (RP) and sensorineural hearing loss (SNHL) caused by mutations in at least 12 genes. Our aim is to identify additional USH-related genes.

METHODS

Clinical examination included visual acuity test, funduscopy and electroretinography. Genetic analysis included homozygosity mapping and whole exome sequencing (WES).

RESULTS

A combination of homozygosity mapping and WES in a large consanguineous family of Iranian Jewish origin revealed nonsense mutations in two ciliary genes: c.3289C>T (p.Q1097*) in C2orf71 and c.3463C>T (p.R1155*) in centrosome-associated protein CEP250 (C-Nap1). The latter has not been associated with any inherited disease and the c.3463C>T mutation was absent in control chromosomes. Patients who were double homozygotes had SNHL accompanied by early-onset and severe RP, while patients who were homozygous for the CEP250 mutation and carried a single mutant C2orf71 allele had SNHL with mild retinal degeneration. No ciliary structural abnormalities in the respiratory system were evident by electron microscopy analysis. CEP250 expression analysis of the mutant allele revealed the generation of a truncated protein lacking the NEK2-phosphorylation region.

CONCLUSIONS

A homozygous nonsense CEP250 mutation, in combination with a heterozygous C2orf71 nonsense mutation, causes an atypical form of USH, characterised by early-onset SNHL and a relatively mild RP. The severe retinal involvement in the double homozygotes indicates an additive effect caused by nonsense mutations in genes encoding ciliary proteins.

Human replication protein A (RP-A) (also known as human single-stranded DNA binding protein, or HSSB) is a multisubunit complex involved in both DNA replication and repair. Potentially important to both these functions, it is also capable of complex formation with the tumor suppressor protein p53. Here we show that although p53 is unable to prevent RP-A from associating with a range of single-stranded DNAs in solution, RP-A is able to strongly inhibit p53 from functioning as a sequence-specific DNA binding protein when the two proteins are complexed. This inhibition, in turn, can be regulated by the presence of various lengths of single-stranded DNAs, as RP-A, when bound to these single-stranded DNAs, is unable to interact with p53. Interestingly, the lengths of single-stranded DNA capable of relieving complex formation between the two proteins represent forms that might be introduced through repair and replicative events. Increasing p53 concentrations can also overcome the inhibition by steady-state levels of RP-A, potentially mimicking cellular points of balance. Finally, it has been shown previously that p53 can itself be stimulated for site-specific DNA binding when complexed through the C terminus with short single strands of DNA, and here we show that p53 stays bound to these short strands even after binding a physiologically relevant site. These results identify a potential dual role for single-stranded DNA in the regulation of DNA binding by p53 and give insights into the p53 response to DNA damage.

Anthocyanin pigments in seed coats of black soybean (Glycine max (L.) Merr.) were extracted with 1% HCl-CH(3)OH, and the crude anthocyanin extract was purified by Shepadex LH-20 and Lichroprep RP-18 open-column chromatography. Three major anthocyanins were isolated, and their chemical structures were identified by spectroscopic methods (UV-visible, FABMS, (1)H and (13)C NMR, and by TLC). The complete structures of these anthocyanins were elucidated as delphinidin-3-glucoside, cyanidin-3-glucoside, and petunidin-3-glucoside. Among them, petunidin-3-glucoside was identified as a new anthocyanin in black soybeans. On the basis of RP-HPLC with a UV-vis detector, the contents of delphinidin-3-glucoside, cyanidin-3-glucoside, petunidin-3-glucoside, and total anthocyanins in seed coats of 10 black soybeans were found in the ranges of 0-3.71, 0.94-15.98, 0-1.41, and 1.58-20.18 mg/g, respectively. The results obtained in this study imply that the seed coats of black soybean can be used as a good source for cyanidin-3-glucoside and delphinidin-3-glucoside.

Reactive oxygen species lead to oxidative damage of the nucleobase and sugar components of nucleotides in double-stranded DNA. The 2-deoxyribonolactone (or oxidized abasic site) lesion results from oxidation of the C-1' position of DNA nucleotides and has been implicated in DNA strand scission, mutagenesis, and covalent cross-linking to DNA binding proteins. We previously described a strategy for the synthesis of DNA-containing deoxyribonolactone lesions. We now report an improved method for the site specific photochemical generation of deoxyribonolactone sites within DNA oligonucleotides and utilize these synthetic oligonucleotides to characterize the products and rates of DNA strand scission at the lactone lesion under simulated physiological conditions. A C-1' nitroveratryl cyanohydrin phosphoramidite analogue was synthesized and used for the preparation of DNA containing a photochemically "caged" lactone precursor. Irradiation at 350 nm quantitatively converted the caged analogue into the deoxyribonolactone lesion. The methodology was validated by RP-HPLC and MALDI-TOF mass spectrometry. Incubation of deoxyribonolactone-containing DNA under simulated physiological conditions gave rise to DNA fragmentation by two consecutive elimination reactions. The DNA-containing products resulting from DNA cleavage at the deoxyribonolactone site were isolated by PAGE and unambiguously characterized by MALDI-TOF MS and chemical fingerprinting assays. The rate of DNA strand scission at the deoxyribonolactone site was measured in single- and double-stranded DNA under simulated physiological conditions: DNA cleavage occurred with a half-life of approximately 20 h in single-stranded DNA and 32-54 h in duplex DNA, dependent on the identity of the deoxynucleotide paired opposite the lesion site. The initial alpha,beta-elimination reaction was shown to be the rate-determining step for the formation of methylene furanone and phosphorylated DNA products. These investigations demonstrated that the deoxyribonolactone site represents a labile lesion under simulated physiological conditions and forms the basis for further studies of the biological effects of this oxidative DNA damage lesion.

Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the processing of the 5' leader sequence of precursor tRNA. We previously found that the reconstituted particle (RP) composed of RNase P RNA and four proteins (Ph1481p, Ph1601p, Ph1771p, and Ph1877p) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 exhibited the RNase P activity, but had a lower optimal temperature (around at 55 degrees C), as compared with 70 degrees C of the authentic RNase P from P. horikoshii [Kouzuma et al., Biochem. Biophys. Res. Commun. 306 (2003) 666-673]. In the present study, we found that addition of a fifth protein Ph1496p, a putative ribosomal protein L7Ae, to RP specifically elevated the optimum temperature to about 70 degrees C comparable to that of the authentic RNase P. Characterization using gel shift assay and chemical probing localized Ph1496p binding sites on two stem-loop structures encompassing nucleotides A116-G201 and G229-CC/D, and box H/ACA. Although we have at present no direct evidence that Ph1496p is a real protein component in the P. horikoshii RNase P, the present result may assign an RNase P protein to L7Ae as a fourth function.

Topologically, platelet factor-4 kinocidins consist of distinct N-terminal extended, C-terminal helical, and interposing gamma-core structural domains. The C-terminal alpha-helices autonomously confer direct microbicidal activity, and the synthetic antimicrobial peptide RP-1 is modeled upon these domains. In this study, the structure of RP-1 was assessed using several complementary techniques. The high-resolution structure of RP-1 was determined by NMR in anionic sodium dodecyl sulfate (SDS) and zwitterionic dodecylphosphocholine (DPC) micelles, which approximate prokaryotic and eukaryotic membranes, respectively. NMR data indicate the peptide assumes an amphipathic alpha-helical backbone conformation in both micelle environments. However, small differences were observed in the side-chain orientations of lysine, tyrosine, and phenylalanine residues in SDS versus DPC environments. NMR experiments with a paramagnetic probe indicated differences in positioning of the peptide within the two micelle types. Molecular dynamics (MD) simulations of the peptide in both micelle types were also performed to add insight into the peptide/micelle interactions and to assess the validity of this technique to predict the structure of peptides in complex with micelles. MD independently predicted RP-1 to interact only peripherally with the DPC micelle, leaving its spherical shape intact. In contrast, RP-1 entered deeply into and significantly distorted the SDS micelle. Overall, the experimental and MD results support a preferential specificity of RP-1 for anionic membranes over zwitterionic membranes. This specificity likely derives from differences in RP-1 interaction with distinct lipid systems, including subtle differences in side chain orientations, rather than gross changes in RP-1 structure in the two lipid environments.

A two-dimensional separation scheme for shotgun proteome analysis employing high-pH reversed-phase HPLC in the first and low-pH ion-pair reversed-phase HPLC in the second dimension (RP x IP-RP-HPLC) has been developed and evaluated. Compared to the classical strong cation exchange x ion-pair reversed-phase (SCX x IP-RP-HPLC) approach, the RP x IP-RP-HPLC system was characterized by a lower degree of orthogonality, which was, however, more than counterbalanced by higher separation efficiency, more homogeneous distribution of peptide elution, and easier experimental handling. Peptide fragment fingerprinting by electrospray-ionization tandem mass spectrometry (ESI-MS/MS) was employed for peptide detection and identification. About 13% more peptides and 7% more proteins could be identified with the alternative approach in 30% less analysis time, enabling the analysis of the proteome of Corynebacterium glutamicum with a coverage of 24.9% (745 proteins). Combining the identification results both of the SCX- x IP-RP-HPLC-ESI-MS/MS and RP- x IP-RP-HPLC-ESI-MS/MS methods, a total of 871 proteins were identified in a cytosolic protein preparation, which represented 29.1% of all proteins annotated in the genome of C. glutamicum.

The regulatory (R) subunit of protein kinase A serves to modulate the activity of protein kinase A in a cAMP-dependent manner and exists in two distinct and structurally dissimilar, end point cAMP-bound "B" and C-subunit-bound "H"-conformations. Here we report mechanistic details of cAMP action as yet unknown through a unique approach combining x-ray crystallography with structural proteomics approaches, amide hydrogen/deuterium exchange and ion mobility mass spectrometry, applied to the study of a stereospecific cAMP phosphorothioate analog and antagonist((Rp)-cAMPS). X-ray crystallography shows cAMP-bound R-subunit in the B form but surprisingly the antagonist Rp-cAMPS-bound R-subunit crystallized in the H conformation, which was previously assumed to be induced only by C-subunit-binding. Apo R-subunit crystallized in the B form as well but amide exchange mass spectrometry showed large differences between apo, agonist and antagonist-bound states of the R-subunit. Further ion mobility reveals the apo R-subunit as an ensemble of multiple conformations with collisional cross-sectional areas spanning both the agonist and antagonist-bound states. Thus contrary to earlier studies that explained the basis for cAMP action through "induced fit" alone, we report evidence for conformational selection, where the ligand-free apo form of the R-subunit exists as an ensemble of both B and H conformations. Although cAMP preferentially binds the B conformation, Rp-cAMPS interestingly binds the H conformation. This reveals the unique importance of the equatorial oxygen of the cyclic phosphate in mediating conformational transitions from H to B forms highlighting a novel approach for rational structure-based drug design. Ideal inhibitors such as Rp-cAMPS are those that preferentially "select" inactive conformations of target proteins by satisfying all "binding" constraints alone without inducing conformational changes necessary for activation.

A novel trypsin inhibitor was extracted from the seeds of Cassia fistula by a process successively involving soaking seeds in water, extraction of the seeds in methanol, and extraction of the cell wall material at high ionic strength. The protease inhibitor (PI) was subsequently purified by chromatography on carboxymethylcellulose, gel filtration and reversed phase HPLC (RP-HPLC). Electrospray ionization mass spectrometry (ESMS) of the oxidized from of the PI yielded an average molecular mass of 5458.6+/-0.8 Da. Edman sequencing of the PI yielded a full-length 50 amino acid sequence inferred to contain eight cysteines and with a calculated average molecular mass (fully oxidized form) of 5459.3 Da, in agreement with the observed mass. The C. fistula seed PI is homologous to the family of plant defensins (gamma-thionins), which have four disulfide linkages at highly conserved locations. The C. fistula PI inhibits trypsin (IC(50) 2 µM), and is the first known example of a plant defensin with protease inhibitory activity, suggesting a possible additional function for some members of this class of plant defensive proteins. C. fistula seeds also contain a 9378 Da lipid transfer protein (LTP) homologue, other LTPs, a 7117 Da protein copurifying with PI activity and a 5144 Da defensin which does not inhibit trypsin. The complete sequence of the 5144 Da defensin was determined by Edman sequencing, yielding a calculated average molecular mass (oxidized form) of 5144.1 Da, in agreement with the mass observed by ESMS. The likely trypsin inhibitory residue on the 5459 Da defensin is Lysine-25, the corresponding amino acid being Tyrosine-25 in the homologous 5144 Da defensin that is not a trypsin inhibitor.

<em>C</em>omplete deficiency of complement <em>C</em>4 is among the strongest genetic risk factors for human systemic lupus erythematosus (SLE). <em>C</em>4 is a constituent of the <em>RP</em>-<em>C</em>4-<em>C</em>YP21-TNX (R<em>C</em><em>C</em>X) module in the human leukocyte antigen (HLA) that exhibits inter-individual copy-number and gene-size variations. Here, we studied two North-African families with complete <em>C</em>4 deficiency and SLE. The first included a Moroccan male SLE patient (1P) and a sibling, who were both homozygous for HLA-A*02 B*17 DRB1*07. The second had an Algerian female SLE patient (2P) homozygous for HLA-A*01 B*17 DRB1*13. Early SLE disease onset, the presence of photosensitive rashes, anti-Ro/SSA, renal disease and high titers of antinuclear antibodies were the common features of complete <em>C</em>4 deficiency. Southern blot analyses showed that 1P had monomodular R<em>C</em><em>C</em>X with a long <em>C</em>4A, whereas 2P had bimodular R<em>C</em><em>C</em>X with one long <em>C</em>4A and one short <em>C</em>4B. Genomic DNA fragments for these mutant genes were amplified and sequenced. A <em>C</em>)T transition that created the R540X nonsense mutation in <em>C</em>4A was found in 1P. An identical 4-bp insertion that generated the Y1537X nonsense mutation was discovered in both <em>C</em>4A and <em>C</em>4B of 2P. The high concordance of SLE and <em>C</em>4 deficiency among patients with non-DR3 and non-DR2 haplotypes underscores the importance of <em>C</em>4 proteins in the protection against SLE.

2D-NOE and 1H NMR chemical shift data obtained for the title oligonucleotides were compared with similar data previously reported [Broido et al. (1985) Eur. J. Biochem. 150, 117-128] for the unmodified "parent" structure, [d(GGAATTCC)]2. The spectroscopically detectable structural perturbations caused by replacement of phosphate oxygen with sulfur were mostly localized within the GsA moiety, and were greater for the Rp configuration wherein sulfur is oriented into the major groove of the B-helix. UV-derived Tm measurements gave the following order of stability for the duplexes in 0.4 M NaCl: unmodified (33.9 +/- 0.1 degrees C) approximately Sp-Sp (34.1 degrees C) greater than Rp-Rp (31.7 degrees C). The title compounds were prepared by a new and convenient synthetic route which utilized HPLC to separate the diastereomeric O-ethyl phosphorothioate precursors, (Rp)- and (Sp)-d[GG(S,Et)AATTCC], for subsequent de-ethylation by ammonia in water.

What's known on the subject? and What does the study add? There are a lot of potential prostate cancer biomarkers being evaluated. All aim to improve on the sensitivity and specificity of PSA. EN2 was recently shown by our group to have better sensitivity and specificity than PSA. EN2 is a simple ELISA test and is not dependent on other parameters, even PSA, unlike all the other current biomarkers under evaluation. To date, no marker correlates with the amount of cancer present - the present study shows this positive correlation with EN2 in men undergoing prostatectomy. The potential utility of this work is that by knowing that the level of EN2 corresponds to the amount of cancer present, irrelevant of tumour grade and number of cancer foci, we can define an EN2 level corresponding to small cancers, which can then undergo surveillance. We are conducting a further study that is aimed at determining whether the levels of EN2 in urine can indicate 'significant' vs 'non-significant cancer' using the threshold of 0.5 mL cancer (after Epstein's work).

OBJECTIVE

To evaluate the relationship between levels of a recently described prostate cancer biomarker engrailed-2 (EN2) in urine and cancer volume in men who had undergone radical prostatectomy (RP) for prostate cancer. To date, prostate-specific antigen (PSA) levels have not reliably predicted prostate cancer volume. Reliable volume indicator biomarker(s) may aid management decisions, e.g. active treatment vs active surveillance.

METHODS

Archived patient samples from the Aarhus Prostate Cancer Project, Denmark, were assessed. Pre-treatment mid-stream urines, without preceding prostatic massage, were collected and stored at -80 °C. Urinary EN2 levels were measured by a recently published enzyme-linked immunosorbent assay.

RESULTS

In all, 88 of the whole cohort of 125 men (70%) were positive for EN2 in their urine (>42.5 µg/L); 38/58 (65%) men where cancer volume data was available. There was no statistical relationship between urinary EN2 levels and serum PSA levels. PSA levels did not correlate with tumour stage, combined Gleason grade, total prostatic weight or cancer volume. There was a strong statistical relationship between urinary EN2 and prostate cancer volume by linear regression (P = 0.006). Higher EN2 levels correlated with tumour stage T1 vs T2 (P = 0.027).

CONCLUSIONS

Pre-surgical urinary EN2 levels were associated with increasing tumour stage and closely reflected the volume of cancer in RP specimens. Given the ease of collection (no prostatic massage required) and the simplicity, low cost and robustness of the assay, EN2 may become a useful biomarker in not only identifying which patients have prostate cancer but may also facilitate risk stratification by indicating the burden of tumour volume.

The C to U editing event that converts an ACG codon to an AUG translation initiation codon in the chloroplast rps 14 transcript is unique to the moss Physcomitrella patens and has not been found in other species. The efficiency of RNA editing was 80% in the young protonemata and decreased to approximately 20% in old protonemata and fully developed leafy shoots. This indicates that RNA editing of this site is regulated in a tissue- and stage-specific manner. In this study, a novel C to U RNA editing site has been identified at the -1 position relative to the AUG. Because the editing site is localized in the mRNA 5' untranslated region, it may affect the efficiency of rps 14 mRNA translation.

A recently developed treatment of reversed-phase column selectivity (the hydrophobic-subtraction model) is reviewed and extended, including its characterization of the selectivity of different column types (e.g., CCC), values of which are summarized here for more than 300 different columns. The selection of columns of either equivalent or different selectivity is readily achievable on the basis of their values of H, S*, etc. The development of the hydrophobic-subtraction model, its use in characterizing the selectivity of different reversed-phase liquid chromatography (RP-LC) columns, and its application to various practical problems as described here began in 1998. The original inspiration for this project owes much to Jack Kirkland, who also contributed actively to the initial studies that laid the foundation of this model; he has since provided other important support to this project. Jack and one of the authors (LRS) have enjoyed a strong professional relationship and personal friendship for the past 35 years, and it is the privilege of the authors to dedicate this paper and the work that it represents to Jack. His contributions to HPLC column technology have extended from the mid-1960s into the present century, and it is impossible to conceive of present day HPLC practice without Jack's contributions over the years. In this and other ways, his position as a pioneer and key implementer of HPLC is widely recognized. We wish Jack well in the years to come.

BACKGROUND

Dysregulation of coagulation is considered a major barrier against successful pig organ xenotransplantation in non-human primates. Inflammation is known to promote activation of coagulation. The role of pro-inflammatory factors as well as the relationship between inflammation and activation of coagulation in xenograft recipients is poorly understood.

METHODS

Baboons received kidney (n=3), heart (n=4), or artery patch (n=8) xenografts from α1,3-galactosyltransferase gene-knockout (GTKO) pigs or GTKO pigs additionally transgenic for human complement-regulatory protein CD46 (GTKO/CD46). Immunosuppression (IS) was based on either CTLA4Ig or anti-CD154 costimulation blockade. Three artery patch recipients did not receive IS. Pro-inflammatory cytokines, chemokines, and coagulation parameters were evaluated in the circulation after transplantation. In artery patch recipients, monocytes and dendritic cells (DC) were monitored in peripheral blood. Expression of tissue factor (TF) and CD40 on monocytes and DC were assessed by flow cytometry. C-reactive protein (C-RP) levels in the blood and C-RP deposition in xenografts as well as native organs were evaluated. Baboon and pig C-RP mRNA in heart and kidney xenografts were evaluated.

RESULTS

In heart and kidney xenograft recipients, the levels of INFγ, TNF-α, IL-12, and IL-8 were not significantly higher after transplantation. However, MCP-1 and IL-6 levels were significantly higher after transplantation, particularly in kidney recipients. Elevated C-RP levels preceded activation of coagulation in heart and kidney recipients, where high levels of C-RP were maintained until the time of euthanasia in both heart and kidney recipients. In artery patch recipients, INFγ, TNF-α, IL-12, IL-8, and MCP-1 were elevated with no IS, while IL-6 was not. With IS, INFγ, TNF-α, IL-12, IL-8, and MCP-1 were reduced, but IL-6 was elevated. Elevated IL-6 levels were observed as early as 2 weeks in artery patch recipients. While IS was associated with reduced thrombin activation, fibrinogen and C-RP levels were increased when IS was given. There was a significant positive correlation between C-RP, IL-6, and fibrinogen levels. Additionally, absolute numbers of monocytes were significantly increased when IS was given, but not without IS. This was associated with increased CD40 and TF expression on CD14+ monocytes and lineage(neg) CD11c+ DC, with increased differentiation of the pro-inflammatory CD14+ CD11c+ monocyte population. At the time of euthanasia, C-RP deposition in kidney and heart xenografts, C-RP positive cells in artery patch xenograft and native lungs were detected. Finally, high levels of both pig and baboon C-RP mRNA were detected in heart and kidney xenografts.

CONCLUSIONS

Inflammatory responses precede activation of coagulation after organ xenotransplantation. Early upregulation of C-RP and IL-6 levels may amplify activation of coagulation through upregulation of TF on innate immune cells. Prevention of systemic inflammation in xenograft recipients (SIXR) may be required to prevent dysregulation of coagulation and avoid excessive IS after xenotransplantation.

Five clustered polyketide synthase (PKS) genes, rifA-rifE, involved in rifamycin (Rf) biosynthesis in Amycolatopsis mediterranei S699 have been cloned and sequenced (August, P.R. et al., 1998. Chem. Biol. 5, 69-79). The five multifunctional polypeptides constitute a type I modular PKS that contains ten modules, each responsible for a specific round of polyketide chain elongation. Sequence comparisons of the Rf PKS proteins with other prokaryotic modular PKSs elucidated the regions that have an important role in enzyme activity and specificity. The beta-ketoacyl:acyl carrier protein synthase (KS) domains show the highest degree of similarity between themselves (86-90%) and to other PKSs (78-85%) among all the constituent domains. Both malonyl-coenzyme A (MCoA) and methylmalonyl-coenzyme A (mMCoA) are substrates for chain elongation steps carried out by the Rf PKS. Since acyltransferase (AT) domains of modular PKSs can distinguish between these two substrates, comparison of the sequence of all ten AT domains of the Rf PKS with those found in the erythromycin (Er) (Donadio, S. and Katz, L., 1992. Gene 111, 51-60) and rapamycin (Rp) (Haydock, S. et al., 1995. FEBS Lett. 374, 246-248) PKSs revealed that the AT domains in module 2 of RifA and module 9 of RifE are specific for MCoA, whereas the other eight modules specify mMCoA. Dehydration of the beta-hydroxyacylthioester intermediates should occur during the reactions catalysed by module 4 of RifB and modules 9 and 10 of RifE, yet only the active site region of module 4 conforms closely to the dehydratase (DH) motifs in the Er and Rp PKSs. The DH domains of modules 9 and 10 diverge significantly from the consensus sequence defined by the Er and Rp PKSs, except for the active site His residues. Deletions in the DH active sites of module 1 in RifA and module 5 in RifB and in the N- and C-terminal regions of module 8 of RifD should inactivate these domains, and module 2 of RifA lacks a DH domain, all of which are consistent with the proposed biosynthesis of Rf. In contrast, module 6 of RifB and module 7 of RifC appear to contain intact DH domains even though DH activity is not apparently required in these modules. Module 2 of RifA lacks a beta-ketoacyl:acyl carrier protein reductase (KR) domain and the one in module 3 has an apparently inactive NADPH binding motif, similar to one found in the Er PKS, while the other eight KR domains of the Rf PKS should be functional. These observations are consistent with biosynthetic predictions. All the acyl carrier protein (ACP) domains, while clearly functional, nevertheless have active site signature sequences distinctive from those of the Er and Rp PKSs. Module 2 of RifA has only the core domains (KS, AT and ACP). The starter unit ligase (SUL) and ACP domains present in the N-terminus of RifA direct the selection and loading of the starter unit, 3-amino-5-hydroxybenzoic acid (AHBA), onto the PKS. AHBA is made by the products of several other genes in the Rf cluster through a variant of the shikimate pathway (August, P.R. et al., inter alia). RifF, produced by the gene immediately downstream of rifE, is thought to catalyse the intramolecular cyclization of the PKS product, thereby forming the ansamacrolide precursor of Rf B. 1998 Elsevier Science B.V.

Sensorineural deafness and retinitis pigmentosa (RP) are the hallmarks of Usher syndrome (USH) but are also prominent features in peroxisomal biogenesis defects (PBDs); both are autosomal recessively inherited. The firstborn son of unrelated parents, who both had sensorineural deafness and RP diagnosed as USH, presented with sensorineural deafness, RP, dysmorphism, developmental delay, hepatomegaly, and hypsarrhythmia and died at age 17 mo. The infant was shown to have a PBD, on the basis of elevated plasma levels of very-long- and branched-chain fatty acids (VLCFAs and BCFAs), deficiency of multiple peroxisomal functions in fibroblasts, and complete absence of peroxisomes in fibroblasts and liver. Surprisingly, both parents had elevated plasma levels of VLCFAs and BCFAs. Fibroblast studies confirmed that both parents had a PBD. The parents' milder phenotypes correlated with relatively mild peroxisomal biochemical dysfunction and with catalase immunofluorescence microscopy demonstrating mosaicism and temperature sensitivity in fibroblasts. The infant and both of his parents belonged to complementation group C. PEX6 gene sequencing revealed mutations on both alleles, in the infant and in his parents. This unique family is the first report of a PBD with which the parents are themselves affected individuals rather than asymptomatic carriers. Because of considerable overlap between USH and milder PBD phenotypes, individuals suspected to have USH should be screened for peroxisomal dysfunction.

OBJECTIVE

To localize and identify the gene and mutations causing autosomal recessive retinitis pigmentosa in three consanguineous Pakistani families.

METHODS

Blood samples were collected and DNA was extracted. A genome-wide scan was performed by using 382 polymorphic microsatellite markers on genomic DNA from affected and unaffected family members, and lod scores were calculated.

RESULTS

A genome-wide scan of 25 families gave an hlod = 4.53 with D8S260. Retinitis pigmentosa in all three families mapped to a 14.21-cM (21.19-Mb) region on chromosome 8 at q11, flanked by D8S532 and D8S260. This region harbors RPch is known to cause autosomal dominant retinitis pigmentosa. Sequencing of the coding exons of RPc.4703delA and c.5400delA, resulting in a frame shift, and a 4-bp insertion, c.1606insTGAA, all causing premature termination of the protein. All affected individuals in these families are homozygous for the mutations. Parents and siblings heterozygous for the mutant allele did not show any signs or symptoms of RP.

CONCLUSIONS

These results provide strong evidence that mutations in RPcan result in recessive as well as dominant retinitis pigmentosa. The findings suggest that truncation of RPRPction, producing a recessive inheritance pattern. In contrast, disruption of RPct and hence a dominant inheritance pattern.

Alpha (alpha) proteobacteria comprise a large and metabolically diverse group. No biochemical or molecular feature is presently known that can distinguish these bacteria from other groups. The evolutionary relationships among this group, which includes numerous pathogens and agriculturally important microbes, are also not understood. Shared conserved inserts and deletions (i.e., indels or signatures) in molecular sequences provide a powerful means for identification of different groups in clear terms, and for evolutionary studies (see www.bacterialphylogeny.com). This review describes, for the first time, a large number of conserved indels in broadly distributed proteins that are distinctive and unifying characteristics of either all alpha-proteobacteria, or many of its constituent subgroups (i.e., orders, families, etc.). These signatures were identified by systematic analyses of proteins found in the Rickettsia prowazekii (RP) genome. Conserved indels that are unique to alpha-proteobacteria are present in the following proteins: Cytochrome c oxidase assembly protein Ctag, PurC, DnaB, ATP synthase alpha-subunit, exonuclease VII, prolipoprotein phosphatidylglycerol transferase, RP-400, FtsK, puruvate phosphate dikinase, cytochrome b, MutY, and homoserine dehydrogenase. The signatures in succinyl-CoA synthetase, cytochrome oxidase I, alanyl-tRNA synthetase, and MutS proteins are found in all alpha-proteobacteria, except the Rickettsiales, indicating that this group has diverged prior to the introduction of these signatures. A number of proteins contain conserved indels that are specific for Rickettsiales (XerD integrase and leucine aminopeptidase), Rickettsiaceae (Mfd, ribosomal protein L19, FtsZ, Sigma 70 and exonuclease VII), or Anaplasmataceae (Tgt and RP-314), and they distinguish these groups from all others. Signatures in DnaA, RP-057, and DNA ligase A are commonly shared by various Rhizobiales, Rhodobacterales, and Caulobacter, suggesting that these groups shared a common ancestor exclusive of other alpha-proteobacteria. A specific relationship between Rhodobacterales and Caulobacter is indicated by a large insert in the Asn-Gln amidotransferase. The Rhizobiales group of species are distinguished from others by a large insert in the Trp-tRNA synthetase. Signature sequences in a number of other proteins (viz. oxoglutarate dehydogenase, succinyl-CoA synthase, LytB, DNA gyrase A, LepA, and Ser-tRNA synthetase) serve to distinguish the Rhizobiaceae, Brucellaceae, and Phyllobacteriaceae families from Bradyrhizobiaceae and Methylobacteriaceae. Based on the distribution patterns of these signatures, it is now possible to logically deduce a model for the branching order among alpha-proteobacteria, which is as follows: Rickettsiales ->> Rhodospirillales-Sphingomonadales ->> Rhodobacterales-Caulobacterales ->> Rhizobiales (Rhizobiaceaea-Brucellaceae-Phyllobacteriaceae, and Bradyrhizobiaceae). The deduced branching order is also consistent with the topologies in the 16 rRNA and other phylogenetic trees. Signature sequences in a number of other proteins provide evidence that alpha-proteobacteria is a late branching taxa within Bacteria, which branched after the delta,epsilon-subdivisions but prior to the beta,gamma-proteobacteria. The shared presence of many of these signatures in the mitochondrial (eukaryotic) homologs also provides evidence of the alpha-proteobacterial ancestry of mitochondria.