Human erythroid porphobilinogen deaminase exists in 2 splice variants

Admixture facilitates genetic adaptations to high altitude in Tibet

Admixture is recognized as a widespread feature of human populations, renewing interest in the possibility that genetic exchange can facilitate adaptations to new environments. Studies of Tibetans revealed candidates for high-altitude adaptations in the EGLN1 and EPAS1 genes, associated with lower haemoglobin concentration. However, the history of these variants or that of Tibetans remains poorly understood. Here we analyse genotype data for the Nepalese Sherpa, and find that Tibetans are a mixture of ancestral populations related to the Sherpa and Han Chinese. EGLN1 and EPAS1 genes show a striking enrichment of high-altitude ancestry in the Tibetan genome, indicating that migrants from low altitude acquired adaptive alleles from the highlanders. Accordingly, the Sherpa and Tibetans share adaptive haemoglobin traits. This admixture-mediated adaptation shares important features with adaptive introgression. Therefore, we identify a novel mechanism, beyond selection on new mutations or on standing variation, through which populations can adapt to local environments.

Molecular diagnostics of acute intermittent porphyria

Acute intermittent porphyria (AIP) is an inherited metabolic disease with an autosomal dominant pattern of inheritance. The disease is caused by a partial deficiency of porphobilinogen deaminase (PBGD) in heme biosynthesis. Since biochemical measurements of patients and their healthy relatives overlap, the diagnosis of AIP may remain undetermined at the symptom-free phase. Mutation detection in AIP, which provides 95% sensitivity and around 100% specificity, has quickly been incorporated into good clinical practice. During an acute attack, which includes various neurovisceral symptoms, measurement of urinary porphobilinogen (PBG) is a method of choice to confirm diagnosis, and DNA testing is unnecessary at that stage. DNA testing has revealed many new patients and excluded AIP from many healthy relatives despite slightly increased excretions of porphyrin precursors and erythrocyte PBGD in the low or borderline zone. Thus, quality-assured DNA testing is accurate enough to confirm or exclude the diagnosis of AIP. The clinical utility of DNA testing is limited for those individuals whose mutation is currently unknown, in which biochemical analyses are essential and the majority of the patients can be identified using urinary PBG and erythrocyte PBGD measurements. The measurement of urinary PBG can be used to evaluate the prognosis for symptom-free individuals. Currently, DNA testing of AIP at the population level is not recommended unless the frequency of gene carriers is locally very high and large-scale population-based mutation screening is reasonable. In the future, the knowledge of gene-gene and gene-environment interactions and protein networks using gene array and proteomics technologies may provide more precise information about pathogenetic mechanisms and novel therapeutic strategies for an acute attack and the long-term complications of AIP. Increasing knowledge of pharmacogenetics may identify the patients who are at high risk for clinical manifestations.

Recovery and stability of RNA in vaginal swabs and blood, semen, and saliva stains

RNA expression patterns, including the presence and relative abundance of particular mRNA species, provide cell and tissue specific information that could be used for body fluid identification. In this report, we address perceived concerns on the stability, and hence recoverability, of RNA in forensic samples. Stains were prepared from blood, saliva, semen, and vaginal secretions and exposed to a range of environmental conditions from 1 to 547 days. The persistence and stability of RNA within each type of body fluid stain were determined by quantitation of total RNA, and reverse transcriptase-polymerase chain reaction (RT-PCR) using eight different mRNA transcripts from selected housekeeping and tissue-specific genes. The results demonstrate that RNA can be recovered from biological stains in sufficient quantity and quality for mRNA analysis. On average, several hundred nanograms of total RNA was recovered from 50-microL-sized blood and saliva stains, 1 microg from a 50-microL semen stain and nearly 70 microg from a whole vaginal swab. Messenger RNA is detectable in some samples stored at room temperature for at least 547 days. The environmental samples that were protected from direct rain impact exhibited housekeeping and tissue specific mRNA recoverability up to 7 days (saliva and semen), 30 days (blood), or 180 days (vaginal swab). Additionally, rain had a detrimental effect on the recoverability of blood (3 days), saliva (1 day), semen (7 days), and vaginal secretions (3 days) specific transcripts, with one of the mRNA species (the semen marker PRM2) not being detectable after 1 day.

Multiplex mRNA profiling for the identification of body fluids

We report the development of a multiplex reverse transcription-polymerase chain reaction (RT-PCR) method for the definitive identification of the body fluids that are commonly encountered in forensic casework analysis, namely blood, saliva, semen, and vaginal secretions. Using selected genes that we have identified as being expressed in a tissue-specific manner we have developed a multiplex RT-PCR assay which is composed of eight body fluid-specific genes and that is optimized for the detection of blood, saliva, semen, and vaginal secretions as single or mixed stains. The genes include beta-spectrin (SPTB) and porphobilinogen deaminase (PBGD) for blood, statherin (STATH) and histatin 3 (HTN3) for saliva, protamine 1 (PRM1) and protamine 2 (PRM2) for semen, and human beta-defensin 1 (HBD-1) and mucin 4 (MUC4) for vaginal secretions. The known or presumed functions of these genes suggest an extremely restricted pattern of gene expression, which is a basic requirement for incorporation into a tissue-specific assay. The methodology is based upon gene expression profiling analysis in which the body fluid-specific genes are identified by detecting the presence of appropriate mRNA species using capillary electrophoresis/laser induced fluorescence. An mRNA-based approach, such as the multiplex RT-PCR method described in the present work, allows for the facile identification of the tissue components present in a body fluid stain and could supplant the battery of serological and biochemical tests currently employed in the forensic serology laboratory.

Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3' boundary sequence spanning 46 kilobases

The mouse immunoglobulin kappa (Igkappa) gene contains an intronic enhancer and two enhancers downstream of its transcription unit. Using chromosome conformation capture technology, we demonstrate that rearranged and actively transcribed Igkappa alleles in MPC-11 plasmacytoma cells exhibit mutual interactions over 22 kb between these three enhancers and Vkappa gene promoters. In addition, the 5' region of the active transcription unit exhibits a continuum of interactions with downstream chromatin segments. We also observe interactions between Ei and E3' with 3' boundary sequences 24 kb downstream of Ed, adjacent to a neighboring housekeeping gene. Very similar interactions between the enhancers are also exhibited by normal B cells isolated from mouse splenic tissue but not by germ line transcriptionally inactive alleles of T cells or P815 mastocytoma cells, which exhibit a seemingly linear chromatin organization. These results fit a looping mechanism for enhancer function like in the beta-globin locus and suggest a dynamic modulation of the spatial organization of the active Igkappa locus. Chromatin immunoprecipitation experiments reveal that the interacting Igkappa gene cis-acting sequences are associated with AP-4, E47, and p65NF-kappaB, potential protein candidates that may be responsible for initiating and/or maintaining the formation of these higher-order complexes. However, S107 plasmacytoma cells that lack NF-kappaB still exhibit mutual interactions between the Igkappa gene enhancers.

Clinical and biochemical characteristics and genotype-phenotype correlation in 143 Finnish and Russian patients with acute intermittent porphyria

Acute intermittent porphyria (AIP), resulting from a deficiency of porphobilinogen deaminase (PBGD) in heme biosynthesis, is genetically heterogeneous and manifests with variable penetrance. The clinical outcome, prognosis, and correlation between PBGD genotype and phenotype were investigated in 143 Finnish and Russian AIP patients with 10 mutations (33G-->T, 97delA, InsAlu333, R149X, R167W, R173W, R173Q, R225G, R225X, 1073delA). Thirty-eight percent of the patients had experienced 1 or more acute attacks during their lives. The proportion of symptomatic patients has decreased dramatically from 49% to 17% among patients diagnosed before and after 1980, respectively. Patients with the R167W and R225G mutations showed lower penetrance (19% and 11%, respectively) and recurrence rate (33% and 0%, respectively) than patients with other mutations (range, 36%-67% and 0%-66%, respectively). Moreover, urinary excretions of porphyrins and their precursors were significantly lower in these patients (porphobilinogen [PBG], 47 +/- 10 vs. 163 +/- 21 micromol/L, p < 0.001; uroporphyrin, 130 +/- 40 vs. 942 +/- 183 nmol/d, p < 0.001). Erythrocyte PBGD activity did not correlate with PBG excretion in remission or with the clinical severity of the disease. Mutations R167W and R225G resulted in milder biochemical abnormalities and clinical symptoms indicating a milder form of AIP in these patients. In all AIP patients, normal PBG excretion predicted freedom from acute attacks. The risk of symptoms was highest for female patients with markedly increased PBG excretion (>100 micromol/L). Proper counseling contributed to the prevention of subsequent attacks in 60% of previously symptomatic and in 95% of previously symptom-free patients.

Rat kidney porphobilinogen deaminase kinetics. Detection of enzyme-substrate complexes

BACKGROUND AND AIMS

Acute intermittent porphyria (AIP) is an inherited disease resulting from a reduced activity of the enzyme porphobilinogen deaminase (PBG-D). The kidney is an important target for numerous porphyrinogenic drugs and it may contribute to the clinical manifestations of porphyric attacks. An evaluation of kidney PBG-D role in the AIP pathophysiology requires detailed information on kidney PBG-D properties, under normal conditions.

METHODS

Rat kidney PBG-D was purified to homogeneity and initial reaction velocities were calculated by measuring uroporphyrinogen I formation at pH 8.2 for different incubation times (0-20 min) and over a wide range of substrate concentrations (0.8-66 microM).

RESULTS

Purified rat kidney PBG-D is a monomeric enzyme showing only a single protein band after SDS-PAGE, Western blot and isoelectric focusing (pI 4.9). Its molecular mass is 40 +/- 2.3 kDa, determined by SDS-PAGE and 39.8 +/- 2 kDa by gel filtration chromatography. Rat kidney PBG-D has an unusual kinetic behaviour, exhibiting a deviation from the Michaelis-Menten hyperbola. PBG-D kinetic data required a fitting to an equation of higher degree, leading to the following apparent kinetic constants: K(1) = 2.08 +/- 0.01 microM and K(2) = 0.102 +/- 0.003 microM.

CONCLUSION

The values of these constants fulfil the restriction 4K(2) < or = K(1)(2), necessary for the occurrence of isoenzymes, interpreted in this work as enzyme-substrate intermediates. The initial reaction velocity expression here defined, correlates with an enzyme carrying only one active site but allowing, through conformational changes, the detection of at least two enzyme-substrate intermediates formed during PBG-D reaction.