The role of HMGA2 in activating the IGFBP2 expression to promote angiogenesis and LUAD metastasis via the PI3K/AKT/VEGFA signaling pathway.

This study investigates the molecular mechanism of HMGA2-mediated regulation of IGFBP2 expression in the PI3K/AKT/VEGFA signaling pathway, which is involved in angiogenesis and LUAD metastasis. Target genes with prognostic implications for LUAD patients were selected using bioinformatics, and previously published literature was referenced to predict the molecular regulatory mechanisms. A549 cells were used for in vitro validation. Cell proliferation and viability were assessed using CCK-8 and EdU assays, while cell migration ability was evaluated using Transwell and wound healing assays. Changes in angiogenesis were examined using an angiogenesis assay. The targeted binding of HMGA2 with the IGFBP2 promoter was confirmed through dual luciferase reporter gene experiments and ChIP assays. In vivo validation was performed using a xenograft mouse model, and changes in angiogenesis and tumor metastasis were observed using western blot, immunofluorescence, and H&E staining. Bioinformatics analysis revealed that HMGA2 was one of the AAGs that differed between normal individuals and LUAD patients and could serve as a critical mRNA for predicting LUAD prognosis. Results from in vitro experiments demonstrated that the expression of the HMGA2 gene was significantly upregulated in LUAD cell lines. Through mediating the expression of IGFBP2, the HMGA2 gene activated the PI3K/AKT/VEGFA signaling pathway, promoting the proliferation, migration, and angiogenesis of A549 cells. In vivo, animal experiments further confirmed that HMGA2 facilitated angiogenesis and the development and metastasis of LUAD through mediating IGFBP2 expression and activating the PI3K/AKT/VEGFA signaling pathway. HMGA2 promotes angiogenesis and healthy growth and metastasis of LUAD by activating the PI3K/AKT/VEGFA signaling pathway by mediating IGFBP2 expression.

Multifunctional Asymmetric Bacterial Cellulose Membrane with Enhanced Anti-Bacterial and Anti-Inflammatory Activities for Promoting Infected Wound Healing.

An asymmetric wound dressing acts as a skin-like structure serves as a protective barrier between a wound and its surroundings. It allows for the absorption of tissue fluids and the release of active substances at the wound site, thus speeding up the healing process. However, the production of such wound dressings requires the acquisition of specialized tools, expensive polymers, and solvents that contain harmful byproducts. In this study, an asymmetric bacterial cellulose (ABC) wound dressing using starch as a porogen has been developed. By incorporating silver-metal organic frameworks (Ag-MOF) and curcumin into the ABC membrane, the wound dressing gains antioxidant, reactive oxygen species (ROS) scavenging, and anti-bacterial activities. Compared to BC-based wound dressings, this dressing promotes efficient dissolution and controlled release of curcumin and silver ions. In a full-thickness skin defect model, wound dressing not only inhibits the growth of bacteria on infected wounds but also regulates the release of curcumin to reduce inflammation and promote the production of epithelium, blood vessels, and collagen. Consequently, this dressing provides superior wound treatment compared to BC-based dressing.

Methane supply drives prokaryotic community assembly and networks at cold seeps of the South China Sea.

Marine cold seeps are unique chemosynthetic habitats fuelled by deeply sourced hydrocarbon-rich fluids discharged at the seafloor. Through oxidizing methane and other hydrocarbons, microorganisms inhabiting cold seeps supply subsurface-derived energy to higher trophic levels, sustaining highly productive oases of life in the deep sea. Despite the central role of microbiota in mediating biogeochemical cycles, the factors that govern the assembly and network of prokaryotic communities in cold seeps remain poorly understood. Here we analysed the geochemical and microbiological profiles of 11 different sediment cores from two spatially distant cold seeps of the South China Sea. We show that prokaryotic communities belonging to the same methane-supply regimes (high-methane-supply, low-methane-supply and non-seep control sediments) had a highly similar community structure, regardless of geographical location, seep-associated biota (mussel, clam, microbial mat) and sediment depth. Methane supply appeared to drive the niche partitioning of anaerobic methanotrophic archaea (ANME) at the regional scale, with ANME-1 accounting for >60% sequence abundance of ANME in the high-methane-supply sediments, while ANME-2 dominated (>90%) the low-methane-supply sediments. Increasing methane supply enhanced the contribution of environmental selection but lessened the contributions of dispersal limitation and drift to overall community assembly. High methane supply, moreover, promoted a more tightly connected, less stable prokaryotic network dominated by positive correlations. Together, these results provide a potentially new framework for understanding the niches and network interplay of prokaryotic communities across different methane seepage regimes in cold-seep sediments.

Mariluticola halotolerans gen. nov., sp. nov., a novel member of the family Devosiaceae isolated from South China Sea sediment.

A novel member of class Alphaproteobacteria was isolated from marine sediment of the South China Sea. Cells of strain LMO-2T were Gram-stain negative, greyish in colour, motile, with a single lateral flagellum and short rod in shape with a slight curve. Strain LMO-2T was positive for oxidase and negative for catalase. The bacterium grew aerobically at 10-40 °C (optimum, 25-30 °C), pH 5.5-10.0 (optimum, pH 7.0) and 0-9 % NaCl (w/v; optimum, 2-3 %). Phylogenetic analysis of the 16S rRNA gene sequence and phylogenomic analysis of the whole genome sequence indicated that strain LMO-2T represents a new genus and a new species within the family Devosiaceae, class Alphaproteobacteria, phylum Pseudomonadota. Comparisons of the 16S rRNA gene sequences of strain LMO-2T showed 94.8 % similarity to its closest relative. The genome size is ~3.45 Mbp with a DNA G+C content of 58.17 mol%. The strain possesses potential capability for the degradation of complex organic matter, i.e. fatty acid and benzoate. The predominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1 ω7c 11-methyl. The sole respiratory quinone was ubiquinone-10. The major identified polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phospholipid. Based on the polyphasic taxonomic data, strain LMO-2T represents a novel genus and a novel species for which the name Mariluticola halotolerans gen. nov., sp. nov., was proposed in the family Devosiaceae. The type strain is LMO-2T (=CGMCC 1.19273T=JCM 34934T).

Prognostic implication of lactic dehydrogenase-to-albumin ratio in critically ill patients with acute kidney injury.

BACKGROUND: No studies have been published on the correlation between lactic dehydrogenase-to-albumin ratio (LAR) and poor prognosis of acute kidney injury (AKI) patients, warranting further research. This analysis sought to investigate the prognostic implication of LAR in critically ill patients with AKI. METHODS: The present study enrolled 11,046 and 5180 adults with AKI from the Medical Information Mart for Intensive Care III (MIMIC III) and MIMIC IV, respectively. Data from MIMIC IV were identified as the training cohort, and those from MIMIC III were identified as the validation cohort. We applied multivariate regression analysis to identify the link between LAR and all-cause mortality. Restricted cubic spline (RCS) was conducted to figure out the correlation between LAR and in-hospital mortality. Furthermore, we carried out stratification analyses to examine if the effects of LAR on in-hospital mortality were consistent across various subclasses. RESULTS: The level of LAR was remarkably higher in the in-hospital non-survivor group (p < 0.001). Furthermore, the increased LAR group presented a remarkably higher rate of in-hospital mortality at AKI stages 1, 2, and 3 compared with the decreased LAR group (all p < 0.001). Multivariate regression analyses exhibited the independent prognostic significance of LAR for all-cause mortality (all p < 0.001). MIMIC III observed concordant results. RCS indicated a non-linear correlation between LAR and in-hospital death (P for non-linearity < 0.001). The relationship between LAR and in-hospital mortality was still significant in patients with various subclasses. CONCLUSIONS: Elevated LAR at admission is a prognostic risk factor for critically ill patients with AKI.

Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin.

Small regulatory RNAs (sRNAs) are present in almost all investigated microbes, regarded as modulators and regulators of gene expression and also known to play their regulatory role in the environmentally significant process. It has been estimated that less than 1% of the microbes in nature are culturable in the laboratory, hindering our understanding of their physiology, and living strategies. However, recent big advancing of DNA sequencing and omics-related data analysis makes the understanding of the genetics, metabolic potentials, even ecological roles of uncultivated microbes possible. In this study, we used a metagenome and metatranscriptome-based integrated approach to identify small RNAs in the microbiome of Guaymas Basin sediments. Hundreds of environmental sRNAs comprising 228 groups were identified based on their homology, 82% of which displayed high similarity with previously known small RNAs in Rfam database, whereas, "18%" are putative novel sRNA motifs. A putative cis-acting sRNA potentially binding to methyl coenzyme M reductase, a key enzyme in methanogenesis or anaerobic oxidation of methane (AOM), was discovered in the genome of ANaerobic MEthane oxidizing archaea group 1 (ANME-1), which were the dominate microbe in the sample. These sRNAs were actively expressed in local Guaymas Basin hydrothermal environment, suggesting important roles of sRNAs in regulating microbial activity in natural environments.

Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea.

A novel methylotrophic methanogen Methanococcoides orientis sp. nov. was isolated from East China Sea sediment. Type strain LMO-1T of Methanococcoides orientis sp. nov. was irregular 1-2 µm cocci without flagella. Strain LMO-1T could utilize a variety of methylated compounds including methanol, methylamine, dimethylamine and trimethylamine for growth and methanogenesis, while H2/CO2 or acetate could not be used for growth or methanogenesis. Optimum growth temperature was 30-35 °C, optimum pH range for growth was 7.0-7.5, while the optimum salinity spectrum for growth was 1.0%-5.0% NaCl. Based on 16S rRNA gene similarity, strain LMO-1T belongs to Methanococcoides, with the highest sequence similarity to Methanococcoides methylutens DSM 2657T (99.8 %), Methanococcoides vulcani SLH33T(99.4 %), followed by Methanococcoides alaskense AK-5T(98.1 %), Methanococcoides burtonii DSM 6242T (98.0 %). Digital DNA-DNA hybridization also showed highest similarity with Methanococcoides methylutens DSM 2657T, with the value of 58.4 %. The average nucleotide identity between strain LMO-1T and Methanococcoides methylutens DSM 2657T was 94.06 %. In summary, LMO-1T represents a novel species of the genus Methaococcoides, for which the name Methanococcoides orientis sp. nov. is proposed. The type strain is LMO-1T (=MCCC 4K00106T=JCM 39195T).

Detection and Gene Mutation Analysis of Three Variations in Two Unrelated Chinese Hereditary Coagulation Factor XI Deficiency Families.

INTRODUCTION: Three variations including a novel F11 gene variation were detected in two unrelated Chinese families with coagulation factor XI deficiency, and their possible pathogenesis was elucidated. METHODS: The genomic DNA of the probands' pedigrees was extracted, and all exons and flanking sequences of F11 gene were subjected to PCR amplification and Sanger sequencing. ClustalX-2.1-win, Mutation Taster, and Swiss-Pdb Viewer software were used to analyze the conservation and impact of the variations on protein function and structure. RESULTS: DNA sequencing showed that the proband one had p.Gly350Glu and p.Trp501stop complex heterozygous variations, while the proband two took p.Pro338Leu and p.Trp501stop compound heterozygous variations. Conservation, structural, and functional analysis of variant amino acids indicated that these three variations were harmful and probably affected the structure and function of the variable protein. CONCLUSIONS: Three variations including p.Pro338Leu, p.Gly350Glu, and p.Trp501stop responsible for the reduction of the FXI activities were herein detected. Notably, the p.Pro338Leu variation was discovered for the first time in the world. Furthermore, the p.Gly350Glu was first reported in China.

Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea.

Methyl-coenzyme M reductase (MCR) has been originally identified to catalyse the final step of the methanogenesis pathway. About 20 years ago anaerobic methane-oxidizing archaea (ANME) were discovered that use MCR enzymes to activate methane. ANME thrive at the thermodynamic limit of life, are slow-growing, and in most cases form syntrophic consortia with sulfate-reducing bacteria. Recently, archaea that have the ability to anaerobically oxidize non-methane multi-carbon alkanes such as ethane and n-butane were described in both enrichment cultures and environmental samples. These anaerobic multi-carbon alkane-oxidizing archaea (ANKA) use enzymes homologous to MCR named alkyl-coenzyme M reductase (ACR). Here we review the recent progresses on the diversity, distribution and functioning of both ANME and ANKA by presenting a detailed MCR/ACR-based phylogeny, compare their metabolic pathways and discuss the gaps in our knowledge of physiology of these organisms. To improve our understanding of alkane oxidation in archaea, we identified three directions for future research: (i) expanding cultivation attempts to validate omics-based metabolic models of yet-uncultured organisms, (ii) performing biochemical and structural analyses of key enzymes to understand thermodynamic and steric constraints and (iii) investigating the evolution of anaerobic alkane metabolisms and their impact on biogeochemical cycles.

Methyl-compounds driven benthic carbon cycling in the sulfate-reducing sediments of South China Sea.

Methane is a potent greenhouse gas; methane production and consumption within seafloor sediments has generated intense interest. Anaerobic oxidation of methane (AOM) and methanogenesis (MOG) primarily occur at the depth of the sulfate-methane transition zone or underlying sediment respectively. Methanogenesis can also occur in the sulfate-reducing sediments through the utilization of non-competitive methylated compounds; however, the occurrence and importance of this process are not fully understood. Here, we combined a variety of data, including geochemical measurements, rate measurements and molecular analyses to demonstrate the presence of a cryptic methane cycle in sulfate-reducing sediments from the continental shelf of the northern South China Sea. The abundance of methanogenic substrates as well as the high MOG rates from methylated compounds indicated that methylotrophic methanogenesis was the dominant methanogenic pathway; this conclusion was further supported by the presence of the methylotrophic genus Methanococcoides. High potential rates of AOM were observed in the sediments, indicating that methane produced in situ could be oxidized simultaneously by AOM, presumably by ANME-2a/b as indicated by 16S rRNA gene analysis. A significant correlation between the relative abundance of methanogens and methanotrophs was observed over sediment depth, indicating that methylotrophic methanogenesis could potentially fuel AOM in this environment. In addition, higher potential rates of AOM than sulfate reduction rates at in situ methane conditions were observed, making alternative electron acceptors important to support AOM in sulfate-reducing sediment. AOM rates were stimulated by the addition of Fe/Mn oxides, suggesting AOM could be partially coupled to metal oxide reduction. These results suggest that methyl-compounds driven methane production drives a cryptic methane cycling and fuels AOM coupled to the reduction of sulfate and other electron acceptors.

Association of neutrophil-to-lymphocyte ratio and risk of cardiovascular or all-cause mortality in chronic kidney disease: a meta-analysis.

BACKGROUND: It is currently controversial whether neutrophil-to-lymphocyte ratio (NLR) has a prognostic role in patients with chronic kidney disease (CKD). We aimed to investigate whether NLR was an independent predictor of cardiovascular or all-cause mortality in CKD patients with or without hemodialysis by performing a meta-analysis. METHODS: Pubmed, Embase, and Cochrane Library databases are systematically searched for relevant literature that investigated NLR and subsequent cardiovascular or all-cause mortality risk in CKD with or without dialysis. Pooled hazard risk (HR) with 95% confidence interval (CI) was calculated for the high vs. low NLR category. RESULTS: A total of thirteen studies enrolling 116,709 patients were identified and analyzed. In summary, high NLR was associated with an increased risk of all-cause mortality (HR 1.93, 95% CI 1.87-2.00; P < 0.00001) and cardiovascular mortality (HR 1.45, 95% CI 1.18-1.79, P < 0.001). Subgroup analysis indicated that high NLR are independently associated with all-cause mortality risk in dialysis patients (HR 1.94, 95% CI 1.87-2.01; P < 0.00001). CONCLUSIONS: This meta-analysis indicates a high NLR is related to all-cause mortality and cardiovascular mortality in patients with chronic kidney disease. Dialysis patients with high NLR are candidates at high risk of mortality to allow for earlier interventions. Further large scale and more rigorously designed studies are warranted to confirm the prognostic value of NLR in the different stages of CKD.

Prognostic factors for ovarian metastases in colorectal cancer patients.

PURPOSE: The aim of this study was to analyze prognostic factors for ovarian metastases (OM) in colorectal cancer (CRC) using data from a Chinese center. In addition, the study aimed at developing a new clinical scoring system for prognosis of OM of CRC patients after surgery. PATIENTS AND METHODS: Data of CRC patients with OM were collected from a single Chinese institution (n = 67). Kaplan-Meier analysis was used to evaluate cumulative survival of patients. Factors associated with prognosis of overall survival (OS) were explored using Cox's proportional hazard regression models. A scoring system to determine effectiveness of prognosis was developed. RESULTS: Median OS values for patients with or without surgery were 22 and 7 months, respectively. Size of OM, number of OM, peritoneal metastasis (PM), Peritoneal cancer index (PCI), and completeness of cytoreduction (CC) were associated with OS of patients through univariate analysis. Multivariate analysis using a Cox regression model showed that only CC was an independent predictor for OS. Three variables (the size of OM >15cm, PCI ≥ 10, and carcinoembryonic antigen (CEA) >30 ng/mL) assigned one point each were used to develop a risk score. The resulting score was used for prognosis of OS. CONCLUSION: Surgical treatment of metastatic sites is effective and safe for CRC patients with OM. CC-0 is recommended for improved prognosis. The scoring system developed in this study is effective for prediction of OS of patients after surgery.

Growth of sedimentary Bathyarchaeota on lignin as an energy source.

Members of the archaeal phylum Bathyarchaeota are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of Bathyarchaeota in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth of Bathyarchaeota Meanwhile, putative bathyarchaeotal tetraether lipids incorporated 13C from 13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth's most abundant biopolymers in anoxic marine sediment.

Risk factors for mortality in hemodialysis patients with COVID-19: a systematic review and meta-analysis.

BACKGROUND: New evidence from studies on risk factors for mortality in hemodialysis (HD) patients with COVID-19 became available. We aimed to review the clinical risk factors for fatal outcomes in these patients. METHODS: We performed meta-analysis using the PubMed, EMBASE, and Cochrane databases. A fixed- or random-effects model was used for calculating heterogeneity. We used contour-enhanced funnel plot and Egger's tests to assess potential publication bias. RESULTS: Twenty-one studies were included. The proportion of males was lower in the survivor group than in the non-survivor group (OR = 0.75, 95% CI [0.61, 0.94]). The proportion of respiratory diseases was significantly lower in the survivor group than in the non-survivor group (OR = 0.42, 95% CI [0.29, 0.60]). The proportion of patients with fever, cough, and dyspnea was significantly lower in the survivor group (fever: OR = 0.53, 95% CI [0.31, 0.92]; cough: OR = 0.50, 95% CI [0.38, 0.65]; dyspnea: OR = 0.25, 95% CI [0.14, 0.47]) than in the non-survivor group. Compared with the non-survivor group, the survivor group had higher albumin and platelet levels and lower leucocyte counts. CONCLUSIONS: Male patients might have a higher risk of developing severe COVID-19. Comorbidities, such as respiratory diseases could also greatly influence the clinical prognosis of COVID-19. Clinical features, such as fever, dyspnea, cough, and abnormal platelet, leucocyte, and albumin levels, could imply eventual death. Our findings will help clinicians identify markers for the detection of high mortality risk in HD patients at an early stage of COVID-19.

Wernicke encephalopathy following advanced caecum cancer.

A 26-year-old lactating mother presented with a 3-week history of abdominal pain, constipation, and vomiting. She denied any history of alcohol abuse or other gastrointestinal problems. Contrast-enhanced CT identified a small-bowel obstruction caused by a cecum cancer (Fig. 1A). Therefore, she underwent right hemicolectomy and ileocolic anastomosis. Post-operatively, she gradually developed drowsiness, fainting, and a rapid heart rate at 130 bpm. However, blood tests were all normal.

Evidences of aromatic degradation dominantly via the phenylacetic acid pathway in marine benthic Thermoprofundales.

Thermoprofundales (Marine Benthic Group D archaea, MBG-D) is a newly proposed archaeal order and widely distributed in global marine sediment, and the members in the order may play a vital role in carbon cycling. However, the lack of pure cultures of these oeganisms has hampered the recognition of their catabolic roles. Here, by constructing high-quality metagenome-assembled genomes (MAGs) of two new subgroups of Thermoprofundales from hydrothermal sediment and predicting their catabolic pathways, we here provide genomic evidences that Thermoprofundales are capable of degrading aromatics via the phenylacetic acid (PAA) pathway. Then, the gene sequences of phenylacetyl-CoA ligase (PCL), a key enzyme for the PAA pathway, were searched in reference genomes. The widespread distribution of PCL genes among 14.9% of archaea and 75.9% of Thermoprofundales further supports the importance of the PAA pathway in archaea, particularly in Thermoprofundales where no ring-cleavage dioxygenases were found. Two PCLs from Thermoprofundales MAGs, PCLM8-3 and PCLM10-15 , were able to convert PAA to phenylacetyl-CoA (PA-CoA) in vitro, demonstrating the involvement of Thermoprofundales in aromatics degradation through PAA via CoA activation. Their acid tolerance (pH 5-7), high-optimum temperatures (60°C and 80°C), thermostability (stable at 60°C and 50°C for 48 h) and broad substrate spectra imply that Thermoprofundales are capable of transforming aromatics under extreme conditions. Together with the evidence of in situ transcriptional activities for most genes related to the aromatics pathway in Thermoprofundales, these genomic, and biochemical evidences highlight the essential role of this ubiquitous and abundant archaeal order in the carbon cycle of marine sediments.

Perspectives on Cultivation Strategies of Archaea.

Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.

Analysis of Metallo-ß-lactamases, oprD Mutation, and Multidrug Resistance of ß-lactam Antibiotic-Resistant Strains of Pseudomonas aeruginosa Isolated from Southern China.

The purpose of this study was to analyze the metallo-ß-lactamases (MBLs) genotype and oprD mutations of the ß-lactam antibiotic-resistant Pseudomonas aeruginosa (PA) strains isolated from southern China. We collected 110 strains of ß-lactam antibiotic-resistant PA from 2 hospitals during January 2016-December 2017 from Dongguan, South China. MBLs were detected, amplified, and typed using EDTA disc synergy test, PCR, and Sanger gene sequencing. The mutations and expression levels of oprD were detected using Sanger gene sequencing and qPCR. A total of 16.36% (18/110) ß-lactam antibiotic-resistant PA strains produced MBLs, and the main genotypes of MBLs were IMP-25, VIM-2, and SIM-2. Sanger gene sequencing results showed that 107 of the 110 strains harbored mutations in oprD sequence, while 3 strains were negative for oprD amplification (2.73%). Among the 107 strains with positive amplification (97.27%), the rate of intentional mutations (including deletions, insertions, and premature stop codons) was 93.46% (100/107) and that of no disrupted mutation was 6.54% (7/107). qPCR analysis confirmed that the expression level of the OprD protein in the 7 strains of no disrupted mutation was significantly reduced. Among the ß-lactam antibiotic-resistant PA strains in southern China, 16.36% were positive for MBLs. The loss rate of oprD was 2.73%, and almost all PA strains showed oprD amplification variation or transcription downregulation. Thus, impaired oprD expression and MBLs production may be some of the mechanisms of ß-lactam antibiotic-resistance of PA strains in southern China.

The trimeric Hef-associated nuclease HAN is a 3'→5' exonuclease and is probably involved in DNA repair.

Nucleases play important roles in nucleic acid metabolism. Some archaea encode a conserved protein known as Hef-associated nuclease (HAN). In addition to its C-terminal DHH nuclease domain, HAN also has three N-terminal domains, including a DnaJ-Zinc-finger, ribosomal protein S1-like, and oligonucleotide/oligosaccharide-binding fold. To further understand HAN's function, we biochemically characterized the enzymatic properties of HAN from Pyrococcus furiosus (PfuHAN), solved the crystal structure of its DHH nuclease domain, and examined its role in DNA repair. Our results show that PfuHAN is a Mn2+-dependent 3'-exonuclease specific to ssDNA and ssRNA with no activity on blunt and 3'-recessive double-stranded DNA. Domain truncation confirmed that the intrinsic nuclease activity is dependent on the C-terminal DHH nuclease domain. The crystal structure of the DHH nuclease domain adopts a trimeric topology, with each subunit adopting a classical DHH phosphoesterase fold. Yeast two hybrid assay confirmed that the DHH domain interacts with the IDR peptide of Hef nuclease. Knockout of the han gene or its C-terminal DHH nuclease domain in Haloferax volcanii resulted in increased sensitivity to the DNA damage reagent MMS. Our results imply that HAN nuclease might be involved in repairing stalled replication forks in archaea.

Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family.

BACKGROUND: Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive. RESULTS: We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, iron homeostasis and DNA repair system genes. Lastly, phylogenomic analysis showed that MTB cluster closely with phototrophic bacteria in this family. One photoheterotrophic genus, Phaeospirillum, clustered within and displays high genomic similarity with Magnetospirillum. Moreover, the phylogenetic tree topologies of magnetosome synthesis genes in MTB and photosynthesis genes in phototrophic bacteria from the Rhodospirillaceae family were reasonably congruent with the phylogenomic tree, suggesting that these two traits were most likely vertically transferred during the evolution of their lineages. CONCLUSION: Our new genomic data indicate that MTB and phototrophic bacteria within the family Rhodospirillaceae possess diversified photoreceptors that may be responsible for phototaxis. Their genomes also contain comprehensive stress response genes to mediate the negative effects caused by illumination. Based on phylogenetic studies, most of MTB and phototrophic bacteria in the Rhodospirillaceae family evolved vertically with magnetosome synthesis and photosynthesis genes. The ancestor of Rhodospirillaceae was likely a magnetotactic phototrophic bacteria, however, gain or loss of magnetotaxis and phototrophic abilities might have occurred during the evolution of ancestral Rhodospirillaceae lineages.