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Analytical Chemistry Aug 2023Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing...
Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the -type oxidase that plays an essential role in adaptation to oxygen-limited conditions in , a model for the clinically relevant, opportunistic pathogen . However, as no comprehensive data were available in , we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond , were predicted to form an operon with a conserved protein and may represent genes. These data demonstrate the power of this combined approach to study small proteins in and show its potential for other prokaryotes.
Topics: Pseudomonas stutzeri; Proteomics; Proteogenomics; Pseudomonas aeruginosa; Oxygen
PubMed: 37535005
DOI: 10.1021/acs.analchem.3c00676 -
Frontiers in Bioscience (Landmark... Jan 2023wilt and blight are the most important diseases of chickpea. The current study was designed to investigate the individual and combined effect of salicylic acid (SA)...
BACKGROUND
wilt and blight are the most important diseases of chickpea. The current study was designed to investigate the individual and combined effect of salicylic acid (SA) with and to suppress wilt and promote growth of chickpea varieties: Thal-2006 and Punjab-2008.
METHODS
At the time of sowing, inoculum of was applied to the soil and the incidence of wilt was recorded after 60 days. The seeds were inoculated with and prior to sowing. Chickpea plants were treated with salicylic acid at seedling stage.
RESULTS
The combination of and SA significantly increased root length (166% and 145%), shoot height (50% and 47%) and shoot biomass (300% and 233%) in cv. Thal-2006 and cv. Punjab-2008, respectively, in infected plants. Similarly, the combined treatment of + SA, also enhanced the plant growth parameters of chickpea varieties. Maximum reduction in disease severity was observed in both + SA (90% and 84%) and + SA (79% and 77%) treatments in cv. Thal-2006 and Punjab-2008, respectively. Both + SA and + SA treatments resulted in increased leaf relative water and total protein content, peroxidase, superoxide dismutase, phenylalanine ammonia-lyase and polyphenol oxidase activities in both resistant (cv. Thal-2006) and susceptible (cv. Punjab-2008) cultivars. Both treatments also significantly reduced malondialdehyde (MDA) and proline content in cv. Thal-2006 and Punjab-2008. Cultivar Thal-2006 was more effective than cv. Punjab-2008.
CONCLUSIONS
The results suggested that, in combination, salicylic acid and may play an important role in controlling wilt diseases by inducing systemic resistance in chickpea.
Topics: Biomass; Cicer; Combined Modality Therapy; Fusarium; Malondialdehyde; Plant Diseases; Salicylic Acid; Pseudomonas; Agricultural Inoculants
PubMed: 36722276
DOI: 10.31083/j.fbl2801020 -
Case Reports in Ophthalmology 2020A patient presented with complaints of a sudden decrease in vision, ocular redness, and pain in the right eye. The patient had a history of clear lens extraction with...
A patient presented with complaints of a sudden decrease in vision, ocular redness, and pain in the right eye. The patient had a history of clear lens extraction with intraocular lens (IOL) implantation for myopia 2 years previously. He had been prescribed topical steroids for episodes of inflammation that occurred repeatedly every 1-2 months. With a presumptive diagnosis of chronic endophthalmitis, a 23-G transconjunctival sutureless pars plana vitrectomy (PPV) with delivery of intravitreal antibiotics was performed the next day. Culture sensitivity testing of the vitreous sample indicated that was sensitive to ceftazidime and gentamicin. Two weeks later, the patient presented with sudden loss of vision and all the signs of recurrent endophthalmitis. 23-G transconjunctival sutureless PPV was performed along with removal of the posterior chamber IOL through a corneal incision. Complete resolution was only achieved after removal of the IOL, resulting in excellent visual recovery. Due to its chronic and fulminating nature, can induce endophthalmitis and should be considered in the differential diagnosis. Aseptic measures are the best prevention.
PubMed: 33437233
DOI: 10.1159/000510129 -
Materials (Basel, Switzerland) Apr 2023Microbiologically influenced corrosion (MIC) is a common phenomenon in water treatment, shipping, construction, marine and other industries. Sulfate-reducing bacteria...
Microbiologically influenced corrosion (MIC) is a common phenomenon in water treatment, shipping, construction, marine and other industries. Sulfate-reducing bacteria (SRB) often lead to MIC. In this paper, a strain of () with the ability to inhibit SRB corrosion is isolated from the soil through enrichment culture. is a short, rod-shaped, white and transparent colony with denitrification ability. Our 16SrDNA sequencing results verify the properties of strains. The growth conditions of bacteria and SRB are similar, and the optimal culture conditions are about 30 °C, pH 7, and the stable stage is reached in about seven days. The bacteria can coexist in the same growth environment. Using the weight loss method, electrochemical experiments and composition analysis techniques we found that can inhibit the corrosion of X70 steel by SRB at 20~40 °C, pH 6~8. Furthermore, long-term tests at 3, 6 and 9 months reveal that can effectively inhibit the corrosion of X70 steel caused by SRB.
PubMed: 37049190
DOI: 10.3390/ma16072896 -
Journal of Ophthalmic Inflammation and... Feb 2024To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
PURPOSE
To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
FINDINGS
A 70-year-old female patient was diagnosed with acute endophthalmitis following intravitreal aflibercept injection for age-related macular degeneration. A standard tap and inject procedure was performed. Microbiological analyses on the anterior chamber and vitreous samples yielded the presence of three non-fermenting Gram-negative rods: Pseudomonas stutzeri, Stenotrophomonas maltophilia, and Ochrobactrum anthropi. The outcome was favorable after intravitreal injections of vancomycin and ceftazidime, with an almost complete recovery of the visual acuity to its baseline level. No potential source of infection was identified.
CONCLUSION
Endophthalmitis following intravitreal injection can be caused by a wide variety of bacteria, including some rare Gram-negative species. They can sometimes co-exist in a single patient, but their virulence may vary greatly. Due to the variable antibiotic susceptibility and frequent multiresistance associated with non-fermenting Gram-negative rods, a prompt microbiological approach is required. Favorable outcome can be achieved with standard management.
PubMed: 38334879
DOI: 10.1186/s12348-023-00376-9 -
Frontiers in Cellular and Infection... 2022The gut microbiota is associated with reproductive disorders in multiple ways. This research investigated possible differences in gut microbiome compositions between...
The gut microbiota is associated with reproductive disorders in multiple ways. This research investigated possible differences in gut microbiome compositions between patients with uterine fibroids (UFs) and healthy control subjects in order to further provide new insight into its etiology. Stool samples were collected from 85 participants, including 42 UF patients (case group) and 43 control subjects (control group). The gut microbiota was examined with 16S rRNA quantitative arrays and bioinformatics analysis. The α-diversity in patients with UFs was significantly lower than that of healthy controls and negatively correlated with the number of tumorigeneses. The microbial composition of the UF patients deviated from the cluster of healthy controls. Stool samples from patients with UFs exhibited significant alterations in terms of multiple bacterial phyla, such as Firmicutes, Proteobacteria, Actinobacteria, and Verrucomicrobia. In differential abundance analysis, some bacteria species were shown to be downregulated (.., , , and ) and upregulated (.., and ). Furthermore, the microbial interactions and networks in UFs exhibited lower connectivity and complexity as well as higher clustering property compared to the controls. Taken together, it is possible that gut microbiota dysbiosis has the potential as a risk factor. This study found that UFs are associated with alterations of the gut microbiome diversity and community network connectivity. It provides a new direction to further explore the host-gut microbiota interplay and to develop management and prevention in UF pathogenesis.
Topics: Dysbiosis; Gastrointestinal Microbiome; Humans; Leiomyoma; RNA, Ribosomal, 16S; Verrucomicrobia
PubMed: 35646718
DOI: 10.3389/fcimb.2022.863594 -
Genes May 2022A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic...
A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic function (ECF) sigma factor AlgU is reported to play key roles in exopolysaccharide (EPS) production and biofilm formation in the genus; however, the function of AlgU in A1501 is still unclear. In this work, we mainly investigated the role of in EPS production, biofilm formation and nitrogenase activity in A1501. The mutant Δ showed a dramatic decrease both in the EPS production and the biofilm formation capabilities. In addition, the biofilm-based nitrogenase activity was reduced by 81.4% in the Δ mutant. The transcriptional level of , a key Psl-like (a major EPS in A1501) synthesis-related gene, was almost completely inhibited in the mutant and was upregulated by 2.8-fold in the -overexpressing strain. A predicted AlgU-binding site was identified in the promoter region of . The DNase I footprinting assays indicated that AlgU could directly bind to the promoter, and β-galactosidase activity analysis further revealed mutations of the AlgU-binding boxes drastically reduced the transcriptional activity of the promoter; moreover, we also demonstrated that AlgU was positively regulated by RpoN at the transcriptional level and negatively regulated by the RNA-binding protein RsmA at the posttranscriptional level. Taken together, these data suggest that AlgU promotes EPS production and nitrogen-fixing biofilm formation by directly activating the transcription of , and the expression of AlgU is controlled by RpoN and RsmA at different regulatory levels.
Topics: Bacterial Proteins; Biofilms; Gene Expression Regulation, Bacterial; Nitrogen; Nitrogenase; Pseudomonas stutzeri; Sigma Factor
PubMed: 35627252
DOI: 10.3390/genes13050867 -
BMC Microbiology May 2022Pseudomonas stutzeri S116 is a sulfur-oxidizing bacteria isolated from marine sludge. It exhibited excellent electricity generation as bioanode and biocathode applied in...
BACKGROUND
Pseudomonas stutzeri S116 is a sulfur-oxidizing bacteria isolated from marine sludge. It exhibited excellent electricity generation as bioanode and biocathode applied in microbial fuel cells (MFCs). Complete genome sequencing of P. stutzeri and cyclic voltammetry method were performed to reveal its mechanism in microbial fuel cells system.
RESULTS
This study indicated that the MFCs generated a maximum output voltage of 254.2 mV and 226.0 mV, and maximum power density of 765 mW/m and 656.6 mW/m respectively. Complete genome sequencing of P. stutzeri S116 was performed to indicate that most function genes showed high similarities with P. stutzeri, and its primary annotations were associated with energy production and conversion (6.84%), amino acid transport and metabolism (6.82%) and inorganic ion transport and metabolism (6.77%). Homology of 36 genes involved in oxidative phosphorylation was detected, which suggests the strain S116 possesses an integrated electron transport chain. Additionally, many genes encoding pilus-assembly proteins and redox mediators (riboflavin and phenazine) were detected in the databases. Thiosulfate oxidization and dissimilatory nitrate reduction were annotated in the sulfur metabolism pathway and nitrogen metabolism pathway, respectively. Gene function analysis and cyclic voltammetry indicated that P. stutzeri probably possesses cellular machinery such as cytochrome c and redox mediators and can perform extracellular electron transfer and produce electricity in MFCs.
CONCLUSION
The redox mediators secreted by P. stutzeri S116 were probably responsible for performance of MFCs. The critical genes and metabolic pathways involved in thiosulfate oxide and nitrate reduction were detected, which indicated that the strain can treat wastewater containing sulfide and nitrite efficiently.
Topics: Bioelectric Energy Sources; Catalysis; Electricity; Electrodes; Nitrates; Pseudomonas stutzeri; Sulfur; Thiosulfates
PubMed: 35590268
DOI: 10.1186/s12866-022-02552-8 -
Plant Physiology and Biochemistry : PPB Oct 2023This study investigated the effect of Pseudomonas stutzeri inoculation on Lemna minor treated with Cu(OH) nanopesticide (NP). The results showed that P. stutzeri...
Pseudomonas stutzeri improves the tolerance of Lemna minor to Cu(OH) nanopesticide by regulating the uptake of copper, antioxidant defense mechanisms, and the expression of metacaspase-1, chlorophyllase, and stress-responsive genes.
This study investigated the effect of Pseudomonas stutzeri inoculation on Lemna minor treated with Cu(OH) nanopesticide (NP). The results showed that P. stutzeri inoculation increased the relative growth rate (RGR) in NP-treated plants. Although chlorophyll and carotenoid contents decreased significantly in NP-treated plants, P. stutzeri inoculation led to an increase in chlorophyll and carotenoid contents in NP-treated plants. Copper (Cu) content increased with increasing NP concentration, but it decreased significantly in the presence of P. stutzeri. NP treatment caused increased HO and TBARS levels, as well as proline levels. However, P. stutzeri inoculation led to decreased HO and TBARS levels and increased SOD, POX, GST, GR, GPX, and DHAR activities. The expression of genes encoding SOD, GST, metacaspase-1, and chlorophyllase was upregulated by NP treatment alone. Additionally, when plants were inoculated with P. stutzeri, the expression of these genes was further enhanced. In conclusion, P. stutzeri inoculation had a positive effect on the growth and antioxidant system of L. minor treated with NP as it enhanced RGR, increased chlorophyll and carotenoid contents, and decreased Cu content and oxidative stress. These findings suggested that P. stutzeri has the potential to promote aquatic plant growth and counteract the negative impacts of NP on these plants.
PubMed: 37699291
DOI: 10.1016/j.plaphy.2023.108002 -
Indian Journal of Ophthalmology Jun 2022To report clinical features, antibiotic susceptibility profile, management, and outcomes of a cluster outbreak of post-cataract surgery Pseudomonas stutzeri...
PURPOSE
To report clinical features, antibiotic susceptibility profile, management, and outcomes of a cluster outbreak of post-cataract surgery Pseudomonas stutzeri endophthalmitis.
METHODS
This was a hospital-based case series in which 14 patients with acute postoperative endophthalmitis who underwent cataract surgery on the same day were included. Based on severity of presentation, they either underwent pars plana vitrectomy (PPV) with intraocular antibiotics (IOAB) or vitreous tap with IOAB. Vitreous aspirates and environmental surveillance samples were inoculated on culture media and further processed by MALDI-TOF MS for identification and Vitek3 for susceptibility profile.
RESULTS
There were 8 females and 6 males with a mean age of 62.14 ± 8.08 years. Presenting signs included corneal folds (100%), hypopyon (57.1%) and fibrin (50%). Ten patients with mild presentation underwent vitreous tap with IOAB. Four patients with severe presentation underwent PPV with IOAB. Pseudomonas stutzeri was isolated from the vitreous samples and was pan-sensitive. Six eyes required multiple interventions. Favorable outcome was obtained in 12 eyes, one eye developed phthisis, and one patient was lost to follow-up.
CONCLUSION
We report the first ever cluster outbreak of Pseudomonas stutzeri endophthalmitis following phacoemulsification with IOL implantation in a single surgeon setting. Majority of the patients had a mild presentation and responded well to targeted anti-microbial treatment.
Topics: Acute Disease; Aged; Anti-Bacterial Agents; Cataract; Disease Outbreaks; Endophthalmitis; Eye Infections, Bacterial; Female; Humans; Male; Middle Aged; Phacoemulsification; Pseudomonas Infections; Pseudomonas stutzeri
PubMed: 35647987
DOI: 10.4103/ijo.IJO_3096_21