Interaction of MCC2, a novel homologue of MCC tumor suppressor, with PDZ-domain Protein AIE-75

AIE-75 is a protein identified as an autoantigen in patients with autoimmune enteropathy and as a colon cancer-related antigen. It has recently been assigned to be a causative gene for Usher type 1C congenital syndromic hearing loss. The novel protein has three PSD-95/Dlg/ZO-1 (PDZ) protein-protein interaction domains and is therefore implicated to function as a molecular anchor or sorter. We have identified a novel protein that binds to AIE-75 by yeast two-hybrid screening. The protein has a high homology to the tumor suppressor MCC (mutated in colon cancer; or MCC1 hereafter) and was named MCC2. MCC2 protein binds the first PDZ domain of AIE-75 with its C-terminal amino acids -DTFL. Since the MCC1 does not bind to AIE-75 and the MCC2 displays different expression patterns in various organs compared to MCC1, they appear to play distinct roles in cells. The MCC2 gene is located on chromosome 19p13 in the vicinity of APCL gene, while MCC1 maps near to APC tumor suppressor gene. Because of negative expression of MCC2 in a panel of cancer cell-lines compared to the corresponding normal tissues, we suggest that further study is necessary to investigate a possible role of MCC2 as a tumor suppressor.

[Direct identification of mycobacteria from the positive cultures in mycobacteria growth indicator tube (MGIT)]

The ability of the AccuProbe (Kyokuto) to identify mycobacteria directly from the positive cultures in an automatic detector for mycobacteria (BACTEC MGIT960, Becton Dickinson) was evaluated. Sputum samples were collected from patients with suspected mycobacteriosis between February and April 1999 and conventionally incubated in MGIT960 (37 degrees C for 42 days). The MGIT-positive cultures were successively incubated for several days and were directly identified with the AccuProbe. Monomycobacterial strains were detected from 93 (93.9%) of the 99 sputum samples and polymycobacterial strains were detected from 6 sputum samples (6.1%). Viable cell counts in the positive cultures in MGIT960 were determined using Middlebrook 7H10 agar. The cell counts of Mycobacterium tuberculosis and Mycobacterium avium-intracellulare complex (MAC) varied greatly among the individual samples; the former, 3.8 x 10(2)-2.5 x 10(6) cfu/ml and the latter 1.5 x 10(3)-1.9 x 10(8) cfu/ml. The great differences in the cell counts were observed among these samples. Although the cultures in MGIT were estimated as positive, the early stage of bacterial growth might be used as the samples for the cell counting. By this method, 96 of the total 101 cases were successfully identified as follows: M. tuberculosis 57 cases (56.4%) and MAC 39 cases (38.6%). In conclusion, the present results indicate that the direct identification of mycobacteria from the positive cultures in MGIT960 using AccuProbe is useful for a rapid diagnosis in microbiological testing for mycobacteriosis which has tended to increase in recent years.

Expression of p53 tumor suppressor gene in adenoid cystic and mucoepidermoid carcinomas of the salivary glands

Seventeen adenoid cystic carcinomas (ACCs) and 27 mucoepidermoid carcinomas (MECs) occurring in the salivary glands were analyzed for p53 tumor suppressor gene alteration (exons 5-8) and protein expression. The cell proliferation activity was also examined by Ki-67 immunohistochemistry. The p53 alterations were detected in three samples (17.6%) of ACC and in four samples (14.8%) of MEC, and were only found in carcinomas arising in the minor salivary glands. The occurrence of the p53 gene alteration is less frequent in ACC and MEC than that in other kinds of tumors, and therefore does not seem to play a critical role in the course of the tumorigenesis in ACC and MEC. All ACC samples arising from the minor salivary glands exhibiting p53 gene alterations showed recurrence/metastasis, thus suggesting a poor outcome of these patients. All ACCs and three out of four MECs samples with p53 gene alterations showed the lowest degree of p53 immunostaining ratio, thus suggesting that no correlation exists between the p53 gene alterations and the p53 immunostaining in these salivary gland carcinomas. No significant relationship was demonstrated between the immunostaining ratio of either p53 or Ki-67 and the morphological growth pattern or patient clinical course in the ACC samples. The p53 immunopositivity in MEC correlated to the histological grade. The Ki-67 immunostaining ratio was also significantly related to the histological grade and the clinical course in MEC.

Detection of antipituitary antibodies in patients with autoimmune thyroid disease

The aim of the present study was to investigate the prevalence of antipituitary antibodies (APA) in patients with autoimmune thyroid disease as determined by Western blot analysis and enzyme-linked immunosorbent assay (ELISA). Results by Western blot analysis showed positivity for APA in serum of 22.4% of patients with Graves' disease (n=143, p<0.05) and 18.5% of patients with Hashimoto's thyroiditis (n=54, p<0.05), which were significantly higher than 6.2% in healthy controls (n=97). Similar results were obtained with ELISA. The titers of APA measured by ELISA (APA/ELISA) remained unchanged before and after therapy with antithyroid drug for Graves' disease, while thyrotropin-binding inhibitor immunoglobulins (TBII) decreased significantly. Similarly, no changes in APA by Western blot analysis were observed after therapy. In patients with Graves' disease, APA were not associated with thyroid status. There was no difference in APA between patients with positive and negative thyroid autoantibodies. A significant but weak positive correlation between APA/ELISA and anti-human GH measured by ELISA (anti-hGH/ELISA) was observed in patients with Graves' disease (r=0.601 p<0.001) and Hashimoto's thyroiditis (r=0.428 p<0.005). These findings have demonstrated the existence of APA detected by Western blot analysis and ELISA in some cases of autoimmune thyroid disease. The present results suggest that hGH and other antigens may be involved in APA in patients with Graves' disease and Hashimoto's thyroiditis.

Hormone replacement therapy increases plasma level of angiotensin II in postmenopausal hypertensive women

The renin-angiotensin-aldosterone system plays a major role in the pathogenesis of hypertension by enhancing the production or the activity of angiotensin II (ANG II). We evaluated the effects of hormone replacement therapy (HRT) on the renin-angiotensin-aldosterone system and on bradykinin in postmenopausal women (PMW) who were hypertensive or normotensive. Subjects included 28 PMW whose elevated blood pressure (BP) was well controlled on antihypertensive agents excluding diuretics, angiotensin-converting enzyme (ACE) inhibitors, and ANG II receptor antagonists. As controls, we evaluated 16 normotensive PMW. All subjects received oral HRT daily for 6 months. The plasma levels of angiotensin I (ANG I), ANG II, and bradykinin as well as plasma renin activity (PRA) showed a significant increase in HRT in the hypertensive group, but not in the normotensive group. The serum ACE activity showed a significant decrease in both groups, but the plasma level of aldosterone was unchanged. Despite the decrease in serum ACE activity, there was an increase in the plasma ANG II level. Hormone replacement therapy increased the level of ANG II in the hypertensive women, but their BP was unaffected. The increase in plasma bradykinin level may maintain homeostasis in the presence of an increase in plasma ANG II, which is a risk factor for cardiovascular disease. Hormone replacement therapy was associated with a decrease in serum ACE and an increase in plasma bradykinin in hypertensive PMW. Accordingly, the protective effect of HRT against cardiovascular disease in PMW can be provided by a decrease in ACE activity and an increase in bradykinin.

The significance of measuring plasma leptin in acute myocardial infarction

We measured leptin concentrations in patients with acute myocardial infarction (AMI, n = 21) and in 15 age-matched controls, and compared leptin concentrations with levels of other myocardial enzymes and indicators of AMI. Blood was sampled immediately after hospital admission and at 1 h, 2 h, 3 h, 6 h and 9 h, then every 12 h until 5 days post-admission. Patients were stratified into three groups according to peak leptin concentrations: hypoleptinaemia (< 3 ng/ml); normoleptinaemia (> or = 3 - < 15 ng/ml) and hyperleptinaemia (> or = 15 ng/ml). Hypoleptinaemic AMI patients had significantly increased concentrations of plasma lactate dehydrogenase compared with normoleptinaemic patients. No significant differences in other serum markers were noted between hyperleptinaemic and normoleptinaemic AMI patients. A significant negative correlation was found between the peak concentrations of leptin and interleukin 6. Leptin may play a role in the regulation of the development of cardiac damage in patients with AMI.

[Classification and pathophysiology of symptomatic obesity]

Symptomatic obesity was classified by 1) endocrine obesity, 2) central nerve-related obesity, 3) genetic syndrome with obesity and 4) drug-induced obesity. Pathogenesis and pathophysiology of the diseases which induce symptomatic obesity, were briefly described. The origins of hyperphagia and obesity in these diseases have not yet clarified. Gene abnormalties of the genetic syndrome with obesity will be elucidated in near future by the rapidly progress of molecular biological techniques.

Markers of undiagnosed incidental cancer in comparison with clinical prostatic cancer

We propose that carcinoembryonic antigen (CEA) may be a tumor marker for prostatic cancer in addition to prostate specific antigen (PSA), gamma-seminoprotein and prostate acid phosphatase (PAP). The tests were done on 15 sera and autopsy specimens of prostatic cancer. Eight of them were clinical cancers and the remaining seven were incidental ones. We measured serum PAP, PSA, CEA and CA 19-9 and immunohistochemically evaluated these specimens. In clinical cancers, serum PAP, PSA, CEA and CA 19-9 were 1272.9 +/- 3094.4, 146.7 +/- 233.6, 36.3 +/- 36.0 and 80.4 +/- 92.0. Immunohistochemically, all were positive for PAP, PSA, CEA and CA 19-9. In incidental cancers, serum PAP, PSA, CEA and CA 19-9 were 2.4 +/- 1.5, 7.9 +/- 16.9, 128.1 +/- 182.7 and 201.8 +/- 416.1. We conclude that the patients with higher levels of plasma PAP or PSA should go through CEA and CA 19-9 measurement in order to diagnose clinical prostatic cancer.

Randomized trial of cisplatin and carboplatin versus cisplatin, vinblastine and bleomycin in ovarian cancer

Between January 1992 and July 1997, 202 cases of epithelial ovarian cancer were registered and assigned randomly to a combination of cisplatin and carboplatin (PP group), or cisplatin, vinblastine and bleomycin (PVB group). We analyzed 189 patients whose clinical records were available. The PP chemotherapeutic regimen was advantageous in terms of overall survival compared to the PVB regimen until 4 years after the initial operation. However, the 5-year survival rates were almost the same in both groups. However, in stage III patients, the mean survival time in the PP group was 51.4 months and that in the PVB group was 23.3 months, and there was a statistically significant difference in the survival curves between the two groups (p = 0.0158). The 5-year survival rates were 31.1 and 20.4% in the PP and PVB groups, respectively, in stage III patients. The PP regimen was also significantly superior in patients with macroscopic residual tumor after the initial operation, and the 5-year survival rates were 25.7 and 10.1% in the PP and PVB groups, respectively (p = 0.0128). However, there was no significant difference between the two regimens in patients without macroscopic residual tumor. Cox's proportional hazards regression analysis showed that tumor stage, presence of macroscopic residual tumor, and the chemotherapeutic regimen used were significant prognostic factors. In conclusion, the PP chemotherapeutic regimen is superior to the PVB regimen especially in the treatment of advanced ovarian cancer.

A case of probable acute interstitial pneumonia with a dramatic response to pulse corticosteroid administration

A 38-year-old Japanese male without any significant respiratory risk factors was admitted to our hospital because of an acute onset of fulminant pneumonia refractory to intravenous antibiotics administration and an unexplained creatine kinase elevation. He was intubated and under ventilator support on the second hospital day, but responded dramatically to i.v. pulse methylprednisone treatment. After exclusion of secondary etiologies including collagen diseases, we concluded this case as a probable acute (idiopathic) interstitial pneumonia, or Hamman-Rich syndrome, responding dramatically to the corticosteroid pulse administration.

Tumor necrosis factor-alpha (TNF-alpha) plays a protective role in acute viralmyocarditis in mice: A study using mice lacking TNF-alpha

BACKGROUND

It has been reported that tumor necrosis factor-alpha (TNF-alpha) is expressed in the heart with viral myocarditis and that its expression aggravates the condition. The pathophysiological effects of TNF-alpha on viral myocarditis, however, have not been fully elucidated.

METHODS AND RESULTS

To investigate the role of TNF-alpha in the progression of viral myocarditis, we used TNF-alpha gene-deficient mice (TNF-alpha(-/-)) and induced acute myocarditis by infection with encephalomyocarditis virus (EMCV). The survival rate of TNF-alpha(-/-) mice after EMCV infection was significantly lower than that of TNF-alpha(+/+) mice (0% versus 67% on day 14). Injection of recombinant human TNF-alpha (0.2 to 4.0 microg/mouse IV) improved the survival of TNF-alpha(-/-) mice in a dose-dependent manner, indicating that TNF-alpha is essential for protection against viral myocarditis. The levels of viral titer and viral genomic RNA of EMCV in the myocardium were significantly higher in TNF-alpha(-/-) than in TNF-alpha(+/+) mice. Histopathological examination showed that the inflammatory changes of the myocardium were less marked in TNF-alpha(-/-) than in TNF-alpha(+/+) mice. Immunohistochemical analysis revealed that the levels of immunoreactivity of intercellular adhesion molecule-1 and vascular cell adhesion molecule-1 in the myocardium were decreased in TNF-alpha(-/-) mice compared with TNF-alpha(+/+) mice.

CONCLUSIONS

These observations suggested that TNF-alpha is necessary for adhesion molecule expression and to recruit leukocytes to inflammatory sites, and thus, the lack of this cytokine resulted in failure of elimination of infectious agents. We concluded that TNF-alpha plays a protective role in the acute stage of viral myocarditis.

Anti-alpha-fodrin autoantibody is an early diagnostic marker for childhood primary Sjögren's syndrome

OBJECTIVE

alpha-fodrin is a recently identified autoantigen associated with adult primary Sjögren's syndrome (SS). We tested whether anti-alpha-fodrin antibody could also be used as a diagnostic marker for childhood SS.

METHODS

We performed immunoblot analysis of sera from 7 patients with childhood primary SS using glutathione-S-transferase alpha-fodrin fusion protein as an antigen.

RESULTS

Anti-alpha-fodrin antibody was detected in sera from all 7 patients with childhood primary SS, 2 of 4 with secondary SS, and one of 7 with systemic lupus erythematosus, but in no other healthy controls.

CONCLUSION

The anti-alpha-fodrin autoantibody was detected before anti-SSA or SSB antibody became positive; thus anti-alpha-fodrin antibody could be a useful marker for the early diagnosis of SS.

KL-6 is a potential marker for interstitial lung disease associated with juvenile dermatomyositis

Serum levels of KL-6 were examined in 8 cases of juvenile dermatomyositis: 3 with interstitial lung disease (ILD) and 5 without ILD. The KL-6 levels were elevated in the ILD cases and correlated with the degree of computed tomography findings. The measurement of serum KL-6 levels is useful for evaluating juvenile dermatomyositis-associated ILD.

Curative resection of both primary and second primary lung cancer

Curative resection of a second primary lung cancer in a patient who survived small-cell lung cancer is reported. Small-cell cancer had been treated with chemotherapy followed by surgical resection 12 years before. The patient developed squamous cell cancer as the second primary tumor and underwent lobectomy with mediastinal node dissection. Patients who undergo two curative pulmonary resections of both primary and second primary lung cancer are extremely rare. The patient is alive 176 months after the initial diagnosis of small-cell lung cancer and 28 months after resection for his second primary lung cancer. Careful follow-up at an interval of 3-6 months beyond 10 years is very important because adequate treatments could lead to longer survival of patients with primary small-cell lung cancer.

Optimal atrioventricular delay setting determined by evoked QT interval in patients with implanted stimulus-T-driven DDDR pacemakers

Cardiac function is improved by optimizing the atrioventricular (AV) delay. An automatic optimizing function of AV delay may be necessary to achieve the most favourable haemodynamic state in paced patients. The QT interval may change when cardiac function is improved by optimizing the AV delay. The QT or stimulus-T interval is used as a sensor for rate-responsive pacemakers. Evoked (e) QT interval is measured as the time duration from the ventricular pace pulse (stimulus) and the T-sense point that is the steepest point of the intracardiac T wave (stimulus-T interval). The relationship between AV delay, eQT interval and cardiac function was studied in 10 patients (73 +/- 10 (SD) years old) with an implanted stimulus-T-driven DDDR pacemaker. Cardiac output (CO) and pulmonary capillary wedge pressure (PCWP) were measured by Swan-Ganz catheter. The AV delay was prolonged stepwise by 30 ms. Electrocardiogram event markers which indicated ventricular spike and sensed T wave were recorded, and the interval between two event markers was measured as eQT interval. When AV delay was changed from 240 ms to the AV delay at which CO was maximal (172 +/- 33 ms), eQT interval prolonged from 346 +/- 60 to 353 +/- 62 ms (P < 0.01). There was a significant positive correlation between the optimal AV delay at which CO was maximal (172 +/- 33 ms) and the optimal AV delay which was predicted from the maximum eQT interval (179 +/- 37 ms, r = 0.92, P < 0.001). When AV delay was changed from 240 ms to the predicted optimal AV delay, CO increased from 4.2 +/- 0.7 to 4.5 +/- 0.81.min-1 (P < 0.001) and PCWP was decreased from 7.1 +/- 4.0 to 5.7 +/- 3.1 mmHg (P < 0.05). In conclusion, the optimal AV delay can be predicted from the eQT interval which is sensed by an implanted pacemaker. Automatic setting of the optimal AV delay may be achieved by the QT sensor of an implanted pacemaker.

Extracellular mechanism through the Edg family of receptors might be responsible for sphingosine-1-phosphate-induced regulation of DNA synthesis and migration of rat aortic smooth-muscle cells

Exogenous sphingosine 1-phosphate (S1P) increased cytosolic Ca(2+) concentration, stimulated thymidine incorporation (DNA synthesis) and inhibited cell migration in rat aortic smooth-muscle cells (AoSMCs). Although exogenous sphingosine, a substrate of sphingosine kinase or a precursor of S1P, markedly induced the intracellular accumulation of S1P, the lipid failed to mimic the S1P-induced actions. In contrast, dihydrosphingosine 1-phosphate (DHS1P), an S1P receptor agonist, duplicated these S1P actions even though DHS1P was approx. 20-50-fold less potent than S1P. The pharmacological properties of DHS1P for the S1P receptor subtypes Edg-1, Edg-3, Edg-5 and Edg-6 were compared in Chinese hamster ovary (CHO) cells that were overexpressing the respective receptor. In these S1P-receptor-overexpressing cells, DHS1P was approx. 20-30-fold less potent than S1P for the displacement of [(3)H]S1P binding and inositol phosphate response in Edg-5-expressing CHO cells, as was the case for AoSMCs. However, it was slightly (not more than 3-fold) less potent than S1P in cells expressing Edg-1, Edg-3 or Edg-6. Of the above-mentioned four types of S1P receptor, Edg-5 was abundantly expressed in AoSMCs, as demonstrated by Northern blotting. These results suggest that the intracellular accumulation of S1P is not necessary for the S1P-induced Ca(2+) response, for the stimulation of DNA synthesis or for the inhibition of cell migration. Thus these S1P-induced actions might be mediated through extracellular (or cell-surface) S1P receptors in AoSMCs: Edg-5 might be a most important receptor subtype.

Spinal tanycytic ependymomas

Three cases of spinal tanycytic ependymoma are reported, a man aged 45 years and two women aged 36 and 55 years. Each patient developed gradual paraparesis over a few months prior to admission. Magnetic resonance imaging showed an enhancing, well-circumscribed tumor in the spinal cord in each case. Histologically, the tumors consisted of monotonous proliferation of long spindle cells with markedly eosinophilic cell processes; focally forming perivascular pseudorosettes. The tumor cells were strongly immunopositive for glial fibrillary acidic protein, S-100 protein and vimentin. Ultrastructurally, in addition to massive intermediate filaments, many tumor cells showed abundant microtubules. Well-developed desmosomes and microvilli/cilia-lined microlumina were occasionally observed. The tumors were grossly totally removed and the patients remain recurrence free at 9, 9, and 2 years postoperatively. Reviewing reported cases including our three cases, tanycytic ependymoma may occur frequently in spinal cord, especially in the cervical region of the spinal cord. Since histologically it resembles pilocytic astrocytoma and schwannoma, tanycytic ependymoma should be included in the differential diagnosis of benign spindle cell tumors of the central nervous system.

Anti-pituitary antibody-induced multiple endocrine disorders in mice

Circulating anti-pituitary antibodies (APAs) have been detected in patients with autoimmune diseases, although the role of autoantibodies in the pathogenesis of autoimmune diseases is still unclear. With the aim of elucidating the autoimmune mechanisms involved in patients with multiple endocrine disorders, we evaluated the pathological changes in the pituitary gland, thyroid, pancreas and adrenal gland of mice, both wild-type and using a murine model of autoimmune thyroid disease [MRL-lpr/lpr] that had been immunized with murine, rat, porcine or human pituitary glands. In four of seven mice, a 22 kD band corresponding to APA was detected by Western blotting in the serum from mice that had been immunized with human pituitary tissues but not in the serum from mice immunized with rat or pig tissue. Inflammatory changes were detected in all groups of mice, occurring in the hypophysis, pancreas and adrenal glands but not in the thyroid. In conclusion, APA-induced autoimmune endocrine disorders are likely to be important for studying the mechanisms involved in autoimmune syndromes.

Optimization of atrioventricular delay and follow-up in a patient with congestive heart failure with an implanted DDD pacemaker: case report

It has been reported that cardiac function can be improved by implanting a DDD pacemaker (PM) and setting a short atrioventricular (AV) delay in patients with impaired cardiac function. A previous report found that the critical AV delay that induces diastolic mitral regurgitation (MR) may represent the upper limit of the optimal AV delay. The optimal AV delay can be predicted by a simple method: slightly prolonged AV delay minus the interval between the end of the atrial kick and complete closure of the mitral valve (duration of diastolic MR) at the AV delay setting. The patient was a 84-year-old man with an old myocardial infarction. He had repeated admissions to hospital for congestive heart failure. ECG showed prolongation of the PQ interval (0.28 s) and complete left bundle branch block. Cardiac function was improved by AV sequential pacing when the AV delay was set at 120ms. After DDD-PM implantation, the cardiothoracic ratio decreased from 57 to 45% and cardiac function was improved from New York Heart Association class III to I. The AV delay was optimized during follow-up. Four years after PM implantation, the patient was in good condition without further hospital admission.

Optically stimulated luminescence from Al2O3:C irradiated with relativistic heavy ions

Optically stimulated luminescence (OSL) from Al2O3:C (ALOC) irradiated with selected heavy ions (4He, 12C, 40Ar, and 56Fe) was examined for discussion on the effectiveness of ALOC for space radiation protection dosimetry. The OSL efficiency on the absorbed dose basis was almost unity for He (LETinfinity x H2O: 2.2 keV x microm(-1)) and decreased with increasing LET for C (14 keV x microm(-1)), Ar (91 keV x microm(-1)), and Fe (198 keV x microm(-1)); a notable reduction greater than 60%, was observed for Fe ions. The linearity in dose response and the angular independence for the heavy ions were fairly good (+/- <15%) Although further experimental studies are clearly necessary, these results suggest that small ALOC chips can be a part of an integrating dosimetry system in future space missions.

Primary intracerebral malignant melanoma with leptomeningeal spread, extradural extension and lung metastasis

A rare primary intracerebral solitary malignant melanoma with extracranial metastasis is reported. The patient was a 66-year-old man who was revealed to have a tumor in the right temporal lobe by MRI. The tumor was totally resected and the histopathological diagnosis was malignant melanoma. Despite postoperative treatment with chemo-radiotherapy, tumor recurred with multiple subarachnoid dissemination. Complete autopsy showed marked leptomeningeal dissemination of tumor in the cerebro-spinal compartment. In the outside of the central nervous system, a microscopic metastatic nodule was found in the right lung. Metastatic tumor in the spinal cord showed the extradural extension which might have led to hematogenous metastasis to the lung.

Diversity of restriction-modification gene homologues in Helicobacter pylori

The complete genome sequences of two Helicobacter pylori strains have recently become available. We have searched them for homologues of restriction-modification genes. One strain (26695) carried 52 such homologues, and the other (J99) carried 53. Their sequence alignments were arranged in the form of a phylogenetic tree and compared with the tree based on rRNA. The trees showed that the homologues are scattered among diverse groups of bacteria. They also revealed high polymorphism within the species--there are 42 pairs with high homology, 10 specific to 26695, and 11 specific to J99. Many of the restriction-modification homologues were characterized by a GC content lower than that of the average gene in the genome. Some of the restriction-modification homologues showed a different codon use bias from the average genes. These observations are interpreted in terms of horizontal transfer of the restriction-modification genes.

Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms

Recent work suggests that restriction-modification gene complexes are mobile genetic elements that insert themselves into the genome and cause various genome rearrangements. In the present work, the complete genome sequences of Pyrococcus horikoshii and Pyrococcus abyssi, two species in a genus of hyperthermophilic archaeon (archaebacterium), were compared to detect large genome polymorphisms linked with restriction-modification gene homologs. Sequence alignments, GC content analysis, and codon usage analysis demonstrated the diversity of these homologs and revealed a possible case of relatively recent acquisition (horizontal transfer). In two cases out of the six large polymorphisms identified, there was insertion of a DNA segment with a modification gene homolog, accompanied by target deletion (simple substitution). In two other cases, homologous DNA segments carrying a modification gene homolog were present at different locations in the two genomes (transposition). In both cases, substitution (insertion/deletion) in one of the two loci was accompanied by inversion of adjacent chromosomal segment. In the fifth case, substitution by a DNA segment carrying type I restriction, modification, and specificity gene homologs was likewise accompanied by adjacent inversion. In the last case, two homologous DNA segments, were found at different loci in the two genomes (transposition), but only one of them had insertion of a modification homolog and an unknown ORF. The possible relationship of these polymorphisms to attack by restriction enzymes on the chromosome will be discussed.