Cytochromes P450 involved in bacterial RiPP biosyntheses.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally synthesized proteins and additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 (P450s) are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of P450s distributed across all domains of life. While the number of characterized P450s involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C-C or C-N bond formation. Formation of some RiPPs is catalyzed by more than one P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered. SUMMARY: The presence of genes encoding P450s in gene clusters for ribosomally synthesized and post-translationally modified peptides expand structural and functional diversity of these secondary metabolites, and here, we review the current state of this knowledge.

More than 20 years' follow-up of metatarsal neck shortening oblique osteotomy for rheumatoid forefoot deformity.

BACKGROUND: In recent years, advances in pharmacotherapy for rheumatoid arthritis (RA) have dramatically improved the control of disease activity. However, a significant number of patients still develop forefoot deformity. The purpose of this study was to investigate the results of more than 20 years' follow-up of metatarsal neck shortening oblique osteotomy (SOO) for forefoot deformity in patients with RA. METHODS: The metatarsal neck SOO was performed on 163 feet in 108 patients between January 1985 and December 1996 in the authors' hospital. For the patients, who met the survey criteria, an observational study was performed clinically and radiologically at the baseline and at more than 20 years after surgery. RESULTS: A retrospective cohort study was conducted on 36 feet in 22 patients, all of whom were female, and the mean age at surgery was 45.6 (35.0-63.0) years old. The follow-up period was 25.1 (21.0-31.0) years. The presence of painful callosities in the surgically treated feet without revised surgeries decreased from 32 feet (100%) to 4 feet (12.5%) at the last follow-up with mild pain that did not cause any footwear problems. Re-osteotomy at the metatarsal of the lessor toe was performed on four feet in two patients. Radiologically, among 128 toes without revised surgeries, 85% were able to have the joint space preserved, and 89% maintained a pain-free condition without any recurrence of deformity. The mean total Japanese Society for Surgery for the Foot (JSSF) RA foot and ankle score was 64.0/100, and the visual analogue scale (VAS) of overall satisfaction was 62 (0: dissatisfied, 100: highly satisfied). The overall satisfaction had a positive correlation with calcaneal pitch and negative correlation with joint space narrowing at the talocrural joint. CONCLUSIONS: Metatarsal neck SOO appeared to be effective for patients with RA. The deformity was corrected and retained for a long time.

More than 10 years' follow-up of the Swanson metacarpophalangeal joint arthroplasty for the rheumatoid hand.

BACKGROUND: In recent years, advances in pharmacotherapy for rheumatoid arthritis have dramatically improved the control of disease activity. However, a significant number of patients still develop hand deformity and require surgical reconstruction. The objective of this study was to evaluate the long-term efficacy and drawbacks of the Swanson metacarpophalangeal joint arthroplasty for patients with rheumatoid arthritis over 10 years. METHODS: Clinical and radiological evaluations were performed for 87 joints of 29 hands in 27 patients who underwent metacarpophalangeal joint arthroplasty using the Swanson implant, and who were followed up for an average of 11.4 (10-14) years. RESULTS: The number of operated tender and swollen metacarpophalangeal joints decreased from 24 (27.6%) and 28 (32.2%) to 1 (1.1%) and 2 (2.3%), respectively. The patients' general health and disease activity score 28-erythrocyte sedimentation rate improved at the last survey. Mild recurrence of ulnar drift was observed, but the deformity was generally well-corrected. Implant fracture was noted in eight joints (9.2%), and revision surgery was performed in two joints (2.3%). The average active range of extension/flexion changed from -46.3°/65.9° to -32.3°/56.6°. While a significant change was not noted in grip or pinch strength, patients were satisfied with the operation especially in terms of pain relief and improved hand appearance. CONCLUSIONS: The long-term results of Swanson metacarpophalangeal joint arthroplasty were good in pain relief and correction of deformity, but some problems remain with regard to implant durability and mobility.

Correction of rheumatoid swan-neck deformity of the finger using the modified Thompson-Littler method.

OBJECTIVES: To investigate the outcomes of the modified Thompson-Littler (m-TL) method, a corrective surgical method utilising a dynamic tenodesis, in patients with rheumatoid swan-neck deformity. METHODS: Twenty-seven fingers in 10 patients with rheumatoid arthritis (RA) underwent surgical correction. The mean age at the time of surgery was 60.3 (45-77) years, the mean duration of RA was 19.3 (4-34) years, and the mean postoperative follow-up period was 2.4 (0.5-6) years. RESULTS: The deformity was corrected and the proximal interphalangeal (PIP) joint pain disappeared in all operated fingers. The mean pinch power between the thumb and the operated finger increased. The active extension decreased, the active flexion increased, and the total arc of motion decreased. Comparing the range of motion by Nalebuff's type classification, the postoperative arc of motion decreased as the type advanced. CONCLUSIONS: The m-TL method provided a favourable outcome in cases of Type ≤III rheumatoid swan-neck deformity without severe joint deterioration at the PIP joint. Aesthetic and functional improvements were observed and the patients were satisfied with the operation.

Arthrodesis of the digital joint using intraosseous wiring in patients with rheumatoid arthritis.

OBJECTIVE: Digital joints affected by rheumatoid arthritis often have severe deformity and/or dislocation, and arthrodesis in a functional position is required. METHODS: Arthrodesis was performed using intraosseous wiring (modified Lister's method) from January 2011 to December 2015, and we investigated the union rate, postoperative complications, and patient satisfaction with the operation at the final follow-up. The DASH score, grip power, and pinch power were also investigated before the operation and at the final follow-up. RESULTS: Arthrodesis was performed for 90 digital joints in 56 patients. Bone union was obtained in 85 of 89 joints (96%). Wire removal was needed due to subcutaneous protrusion in 20 joints and superficial infection in five joints. The mean preoperative DASH score of 50.5 improved to 45.2 at the final follow-up. The pulp pinch power of the index fingers through the little fingers changed significantly. In the questionnaire regarding the operated digit using a visual analogue scale (VAS, 0 [worst] to 100 [best]), the overall satisfaction was 70. CONCLUSION: With this approach, we achieved painless stability as well as deformity correction. A restored prehensile pattern and improvement in the activities of daily life can thus be expected after surgery.

Twenty years' follow-up of radiocarpal arthrodesis for rheumatoid wrists.

OBJECTIVES: A pain-free stable wrist is a prerequisite for patients with rheumatoid arthritis to improve their activity of daily life. The present study investigated whether or not radiocarpal arthrodesis yielded good results for more than 20 years. METHODS: A retrospective study was performed on 20 unstable wrists in 17 patients with rheumatoid arthritis. Radiocarpal arthrodesis combined with synovectomy and the Darrach procedure was performed. Wrist pain, grip power, the range of motion, pharmacotherapy, ESR, CRP, and serial radiographs were investigated at the baseline and 20 years after the operation. Patient-reported outcomes using the mHAQ, DASH and patient's satisfaction level were investigated at the final follow-up. RESULTS: Pain had disappeared completely in all patients at 20 years after the operation. The average grip power increased in 16 wrists (80%) and decreased in 4 wrists (20%). Wrist extension and flexion significantly decreased, and supination and pronation remained within the functional range. Radiographically, ulnar shift and palmar subluxation initially improved and remained unchanged for a long time. Fourteen patients (82.4%) with 17 wrists were satisfied with this operation. CONCLUSION: Radiocarpal arthrodesis for rheumatoid wrists provided painless stability for a long period for 20 years or more.

[A Case of Adenoid Cystic Carcinoma of the Breast].

Primary adenoid cystic carcinoma(ACC)of the breast is a rare type of breast cancer. A 53-year-old woman with a right breast mass was examined at our institute. Ultrasonography showed 12.5×10.3×8.4 mm sized an ill-defined hypoechoic mass at zone C of the right breast. Pathological examination of core needle biopsy revealed atypical cells with solid and cribriform growth pattern. Computed tomography did not reveal lymph node metastases or distant metastases. The preoperative diagnosis was Stage ⅠA(cT1cN0M0, ER/PgR/HER2=-/-/1+)invasive ductal carcinoma or ACC. Surgery consisted of breast-conserving surgery and sentinel node biopsy. Pathological examination of the excised specimen revealed a so- called adenoid cystic pattern, so the final diagnosis was Stage ⅠA(pT1cN0M0, ER/PgR/HER2=-/-/1+)ACC. After 1 year of observation without adjuvant treatment, there has been no recurrence.

Changes in radiographic findings and plantar pressure distribution following forefoot reconstructive surgery for patients with rheumatoid arthritis.

Objectives: To evaluate changes in radiographic findings and plantar pressure distribution after rheumatoid forefoot surgery.Methods: This study was performed on patients with rheumatoid arthritis (RA) who underwent Swanson implant arthroplasty for the 1st metatarsophalangeal (MTP) joint combined with shortening oblique osteotomy at the 2nd through 5th metatarsal necks (group Sw, 55 feet). The following two groups were used as controls: group NS, consisting of 75 feet in RA patients without scheduled forefoot surgery, and group HC, consisting of 24 feet in healthy female subjects. Plantar pressure distribution, and radiographic findings of hallux valgus angle, the angle between the metatarsal bones, talocalcaneal angle, calcaneal pitch angle and calcaneo-first metatarsal angle (CFMA) were measured pre- and one year postoperatively. Peak pressure was measured in nine sections.Results: Calcaneal pitch angle decreased and CFMA increased in group Sw. Peak pressure at the 1st interphalangeal joint (IP) and the 2nd and 3rd MTPs in group Sw decreased, while that at midfoot increased.Conclusion: While the clinical outcome in group Sw was favorable, postoperative longitudinal arch decreased. Postoperative peak pressure at the 2nd through 5th MTPs was comparable with that in group NS; however, it was significantly lower than that in group HC.

Nutritional status as the risk factor of serious infection in patients with rheumatoid arthritis.

Objectives: The aim of this study was to identify the risk factors associated with severe infection in RA patients, with a particular focus on the association of the nutritional status.Methods: We retrospectively analyzed data from 74 patients with RA (male, n = 21; female, n = 53; age 74.2 ± 12.4) admitted to our hospital between 2016 and 2017 for infection (infection group). We also recruited control RA patients (n = 222) who were matched for age, gender and disease duration, with a match ratio of 1:3 (non-infection group). The nutritional condition was assessed based on controlling nutrition status (CONUT) score, and prognostic nutritional index (PNI). The data of the infection group were obtained from the most recent visit prior to the present admission, and non-infection group from the last regular visit in 2017.Results: The respiratory tract was the most frequent site of infection. The BMI and PNI were significantly lower and the CONUT score significantly higher in the infection group than in the non-infection group. A logistic regression analysis revealed that the CONUT score, underlying lung disease and use of prednisolone and biological disease-modifying anti-rheumatic drugs were independent and significant risk factors for serious infection.Conclusion: Poor nutritional status increases the risk of serious infection.

New voyages to explore the natural product galaxy.

Natural products are a large family of diverse and complex chemical molecules that have roles in both primary and secondary metabolism, and over 210,000 natural products have been described. Secondary metabolite natural products are of high commercial and societal value with therapeutic uses as antibiotics, antifungals, antitumor and antiparasitic products and in agriculture as products for crop protection and animal health. There is a resurgence of activity in exploring natural products for a wide range of applications, due to not only increasing antibiotic resistance, but the advent of next-generation genome sequencing and new technologies to interrogate and investigate natural product biosynthesis. Genome mining has revealed a previously undiscovered richness of biosynthetic potential in novel biosynthetic gene clusters for natural products. Complementing these computational processes are new experimental platforms that are being developed and deployed to access new natural products.

Overall benefits provided by orthopedic surgical intervention in patients with rheumatoid arthritis.

OBJECTIVES: To clarify systemic effects of orthopedic surgical intervention in patients with rheumatoid arthritis (RA). METHODS: A prospective observational cohort study was performed in RA patients who were scheduled to have primary elective orthopedic surgeries. Assessments were performed at baseline, 6 and 12 months after surgery using J-HAQ, General Health, EQ-5D, BDI-II, DAS28-CRP(4) and CRP for all registered patients, DASH and grip power for patients with upper-extremity surgeries, TUG for patients with lower-extremity surgeries, and JSSF for patients with ankle and forefoot surgeries. RESULTS: There were 294 sites in 276 patients whose average age was 64 (19-89) years and average disease duration was 16 (1-60) years. Surgical site was shoulder in six patients, elbow in 26, wrist in 74, hand in 63, hip in 13, knee in 50, ankle in 12, and forefoot in 50. In total, physical function (J-HAQ, grip power, DASH, TUG, JSSF), quality of life (J-HAQ, General Health, EQ-5D) and depression (BDI-II) improved and disease activity (CRP, DAS28-CRP(4)) decreased significantly 6 and 12 months after surgery (p<.01), despite some differences in their outcomes by the preoperative disease activity and the surgical site. CONCLUSION: Overall benefits were provided by orthopedic surgical intervention generally in patients with RA.

The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism.

CouR, a MarR-type transcriptional repressor, regulates the cou genes, encoding p-hydroxycinnamate catabolism in the soil bacterium Rhodococcus jostii RHA1. The CouR dimer bound two molecules of the catabolite p-coumaroyl-CoA (Kd = 11 ± 1 µM). The presence of p-coumaroyl-CoA, but neither p-coumarate nor CoASH, abrogated CouR's binding to its operator DNA in vitro. The crystal structures of ligand-free CouR and its p-coumaroyl-CoA-bound form showed no significant conformational differences, in contrast to other MarR regulators. The CouR-p-coumaroyl-CoA structure revealed two ligand molecules bound to the CouR dimer with their phenolic moieties occupying equivalent hydrophobic pockets in each protomer and their CoA moieties adopting non-equivalent positions to mask the regulator's predicted DNA-binding surface. More specifically, the CoA phosphates formed salt bridges with predicted DNA-binding residues Arg36 and Arg38, changing the overall charge of the DNA-binding surface. The substitution of either arginine with alanine completely abrogated the ability of CouR to bind DNA. By contrast, the R36A/R38A double variant retained a relatively high affinity for p-coumaroyl-CoA (Kd = 89 ± 6 µM). Together, our data point to a novel mechanism of action in which the ligand abrogates the repressor's ability to bind DNA by steric occlusion of key DNA-binding residues and charge repulsion of the DNA backbone.

Efficacy and safety of infliximab: A comparison with other biological disease-modifying anti-rheumatic drugs.

OBJECTIVES: The intensification of infliximab (IFX) treatment, involving escalation of the dose and shortening of interval, was approved in Japan in July 2009. We consider IFX intensification therapy to be preferable for patients with treatment-resistant active rheumatoid arthritis (RA). We retrospectively compared the efficacy of IFX with that of other bDMARDs in methotrexate (MTX)-resistant patients. METHODS: Patients who satisfied the following criteria were enrolled: (i) those who started bDMARDs between February 2011 and December 2016, and (ii) those who required bDMARDs after 180 d of MTX treatment. We compared 33 patients who had been treated with IFX (IFX group) and 146 who had received other bDMARDs treatment (non-IFX group). RESULTS: IFX was administered at a dose of 6.98 mg/kg/8-week equivalent at 52 weeks. Clinical disease activity index clinical remission (CDAI-CR) was achieved in 49 of the 179 patients at 52 weeks and 13 of these 49 patients received IFX. Logistic regression analysis showed that treatment with IFX was an important variable for the achievement of CDAI-CR at 52 weeks (odds ratio 2.69, 95% confidence interval 1.13-6.42). The severity and frequency of adverse events did not differ. CONCLUSION: Intensification of IFX was effective and well tolerated for MTX resistant patients.

Plantar pressure and surgical indication of toe arthroplasty for rheumatoid forefoot deformity.

OBJECTIVES: The objective of this study is to clarify the surgical indication for rheumatoid forefoot deformity according to background characteristics and plantar pressure. METHODS: Patients with rheumatoid arthritis were divided into a non-surgical group (group N) and a surgical group (group S). The former consisted of 225 ft, and the latter consisted of 88 ft. DAS28, Japanese Society for Surgery of the Foot rheumatoid arthritis foot and ankle scale (JSSF scale) and hallux valgus angle (HVA) were evaluated as background characteristics. Distribution of peak pressure as plantar pressure was measured in nine sections. RESULTS: In groups N and S, the mean DAS28 was 3.6 and 3.0, the mean JSSF scale was 81.1 and 63.0, and the mean HVA was 19.9° and 35.3°, respectively. The mean peak pressure of group S at the first and third metatarsophalangeal joints was significantly higher compared with group N. Significant differences between the two groups were also seen in Δ pressure (the difference between the maximum and minimum peak pressure values). The cut-off values were 75.0 for JSSF scale, 24.9° for HVA and 3.94 kg/cm2 for Δ pressure. CONCLUSIONS: The combined assessment of HVA and Δ pressure was found to be useful as an indication for surgical treatment of the forefoot.

A preoperative low nutritional prognostic index correlates with the incidence of incisional surgical site infections after bowel resection in patients with Crohn's disease.

PURPOSE: The incidence of incisional surgical site infections (SSIs) is reported to be higher among patients with Crohn's disease (CD) than among those with colorectal cancer. It has also been reported that the preoperative nutritional and inflammatory status is associated with the frequency of postoperative complications. Onodera's prognostic nutritional index (OPNI) is a simple and useful parameter for determining the nutritional and inflammatory status. In the present study, we retrospectively investigated the correlation between the OPNI and the incidence of incisional SSI in patients with CD who had undergone bowel resection. METHODS: A total of 177 CD patients who underwent abdominal surgery were enrolled. Various clinical factors and the OPNI values were evaluated to identify risk factors for incisional SSIs. RESULTS: The incidence of incisional SSIs was 19.8 %. A multivariate analysis indicated that the OPNI was an independent risk factor for incisional SSIs. CONCLUSIONS: The results of this retrospective study suggest that the OPNI is an independent risk factor for incisional SSIs in patients with a history of bowel resection for CD.

Characterization of p-hydroxycinnamate catabolism in a soil Actinobacterium.

p-Hydroxycinnamates, such as ferulate and p-coumarate, are components of plant cell walls and have a number of commercial applications. Rhodococcus jostii RHA1 (RHA1) catabolizes ferulate via vanillate and the ß-ketoadipate pathway. Here, we used transcriptomics to identify genes in RHA1 that are upregulated during growth on ferulate versus benzoate. The upregulated genes included three transcriptional units predicted to encode the uptake and ß-oxidative deacetylation of p-hydroxycinnamates: couHTL, couNOM, and couR. Neither ΔcouL mutants nor ΔcouO mutants grew on p-hydroxycinnamates, but they did grow on vanillate. Among several p-hydroxycinnamates, CouL catalyzed the thioesterification of p-coumarate and caffeate most efficiently (k(cat)/K(m) = ∼ 400 mM(-1) s(-1)). p-Coumarate was also RHA1's preferred growth substrate, suggesting that CouL is a determinant of the pathway's specificity. CouL did not catalyze the activation of sinapate, in similarity to two p-coumaric acid:coenzyme A (CoA) ligases from plants, and contains the same bulged loop that helps determine substrate specificity in the plant homologues. The couO mutant accumulated 4-hydroxy-3-methoxyphenyl-ß-ketopropionate in the culture supernatant when incubated with ferulate, supporting ß-oxidative deacetylation. This phenotype was not complemented with a D257N variant of CouO, consistent with the predicted role of Asp257 as a metal ligand in this amidohydrolase superfamily member. These data suggest that CouO functionally replaces the ß-ketothiolase and acyl-CoA thioesterase that occur in canonical ß-oxidative pathways. Finally, the transcriptomics data suggest the involvement of two distinct formaldehyde detoxification pathways in vanillate catabolism and identify a eugenol catabolic pathway. The results of this study augment our understanding of the bacterial catabolism of aromatics from renewable feedstocks.

An alternative sigma factor governs the principal sigma factor in Streptomyces griseus.

In bacteria, the RNA polymerase holoenzyme comprises a five-subunit core enzyme and a dissociable subunit, sigma factor, which is responsible for transcriptional initiation. The filamentous bacterium Streptomyces griseus has 52 sigma factors, including one essential 'principal' sigma factor (σ(HrdB) ) that is responsible for the transcription of housekeeping genes. Here we characterized an alternative sigma factor (σ(ShbA) ), which is highly conserved within the genus Streptomyces. A σ(ShbA) -deficient mutant showed a severe growth defect and transcriptome analysis indicated that many housekeeping genes were downregulated in response to insufficient σ(ShbA) production. Biochemical and genetic analyses proved that σ(ShbA) is a major determinant of transcription of the σ(HrdB) gene. This observation of a principal sigma factor being governed by another sigma factor throughout growth is unprecedented. We found that increasing σ(ShbA) production with mycelial growth maintained a high σ(HrdB) level late in growth. Furthermore, a hrdB-autoregulatable σ(ShbA) -deficient mutant, in which the principal sigma factor gene can be transcribed by RNA polymerase containing σ(HrdB) itself, showed several defects: rapid mycelial lysis in stationary phase in liquid culture and delayed morphological development and impaired streptomycin production in solid culture. From these observations, we discuss the biological significance of control of σ(HrdB) by σ(ShbA) in S. griseus.

Regulation of the KstR2 regulon of Mycobacterium tuberculosis by a cholesterol catabolite.

Cholesterol catabolism is widespread in actinobacteria and is critical for Mycobacterium tuberculosis (Mtb) virulence. Catabolism of steroid nucleus rings C and D is poorly understood: it is initiated by the CoA thioesterification of 3aα-H-4α(3'-propanoate)-7aß-methylhexahydro-1,5-indanedione (HIP) by FadD3, whose gene is part of the KstR2 regulon. In Mtb, genes of this regulon were upregulated up to 30- and 22-fold during growth on cholesterol and HIP, respectively, versus another minimal medium. In contrast, genes involved in degrading the cholesterol side-chain and nucleus rings A and B were only upregulated during growth on cholesterol. Similar results were obtained in Rhodococcus jostii RHA1. Moreover, the regulon was not upregulated in a ΔfadD3 mutant unable to produce HIP-CoA. In electrophoretic mobility shift assays, HIP-CoA relieved the binding of KstR2(Mtb) to each of three KstR2 boxes: CoASH, HIP and a related CoA thioester did not. Inspection of the structure of KstR2(RHA1) revealed no obvious HIP-CoA binding pocket. The results establish that Mtb can catabolize the entire cholesterol molecule and that HIP-CoA is an effector of KstR2. They further indicate that KstR2 specifically represses the expression of the HIP degradation genes in actinobacteria, which encode a lower pathway involved in the catabolism of multiple steroids.

Low nutritional prognostic index correlates with poor survival in patients with stage IV colorectal cancer following palliative resection of the primary tumor.

BACKGROUND: We retrospectively investigated the prognostic significance of various clinicopathological factors and preoperative nutritional status to select patients with stage IV colorectal cancer (CRC) who will have a poor prognosis after palliative resection of the primary tumor. METHODS: A total of 100 stage IV CRC patients who underwent palliative resection were enrolled. Various clinicopathological factors and Onodera's prognostic nutritional index (OPNI) were evaluated to identify any possible relationship with the prognosis. RESULTS: At the time of the analysis, 83 patients had died, and the median survival time was 21 months. Of the 100 patients, 24 had primary tumor-related symptoms such as obstruction or bleeding. No significant correlation was noted between the OPNI and various clinicopathological factors. The multivariate analysis of patients without primary tumor-related symptoms revealed that the OPNI was an independent prognostic factor. The overall survival of the low-OPNI group was significantly worse than that of the high-OPNI group. CONCLUSIONS: This retrospective study suggested that patients with a low OPNI may not be candidates for palliative resection, because it provides no survival benefit to these patients.