Bacterial natural product biosynthetic genes, canonically clustered, have been increasingly found to rely on hidden enzymes encoded elsewhere in the genome for completion of biosynthesis. The study ...and application of lanthipeptides are frequently hindered by unclustered protease genes required for final maturation. Here, we establish a global correlation network bridging the gap between lanthipeptide precursors and hidden proteases. Applying our analysis to 161,954 bacterial genomes, we establish 5209 correlations between precursors and hidden proteases, with 91 prioritized. We use network predictions and co-expression analysis to reveal a previously missing protease for the maturation of class I lanthipeptide paenilan. We further discover widely distributed bacterial M16B metallopeptidases of previously unclear biological function as a new family of lanthipeptide proteases. We show the involvement of a pair of bifunctional M16B proteases in the production of previously unreported class III lanthipeptides with high substrate specificity. Together, these results demonstrate the strength of our correlational networking approach to the discovery of hidden lanthipeptide proteases and potentially other missing enzymes for natural products biosynthesis.
Thiosulfate oxidation by microbes has a major impact on global sulfur cycling. Here, we provide evidence that bacteria within various Roseobacter lineages are important for thiosulfate oxidation in ...marine biofilms. We isolate and sequence the genomes of 54 biofilm-associated Roseobacter strains, finding conserved sox gene clusters for thiosulfate oxidation and plasmids, pointing to a niche-specific lifestyle. Analysis of global ocean metagenomic data suggests that Roseobacter strains are abundant in biofilms and mats on various substrates, including stones, artificial surfaces, plant roots, and hydrothermal vent chimneys. Metatranscriptomic analysis indicates that the majority of active sox genes in biofilms belong to Roseobacter strains. Furthermore, we show that Roseobacter strains can grow and oxidize thiosulfate to sulfate under both aerobic and anaerobic conditions. Transcriptomic and membrane proteomic analyses of biofilms formed by a representative strain indicate that thiosulfate induces sox gene expression and alterations in cell membrane protein composition, and promotes biofilm formation and anaerobic respiration. We propose that bacteria of the Roseobacter group are major thiosulfate-oxidizers in marine biofilms, where anaerobic thiosulfate metabolism is preferred.
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the ...request of the Editors-in-Chief.
After a thorough investigation, the Editors have concluded that the acceptance of this article was partly based upon the positive advice of one illegitimate reviewer report. The report was submitted from an email account which was provided to the journal as a suggested reviewer during the submission of the article. Although purportedly a real reviewer account, the Editors have concluded that this was not of an appropriate, independent reviewer.
This manipulation of the peer-review process represents a clear violation of the fundamentals of peer review, our publishing policies, and publishing ethics standards. Apologies are offered to the reviewer whose identity was assumed and to the readers of the journal that this deception was not detected during the submission process.
Lactic acid bacteria (LAB) produce various bioactive secondary metabolites (SMs), which endow LAB with a protective role for the host. However, the biosynthetic potentials of LAB-derived SMs remain ...elusive, particularly in their diversity, abundance, and distribution in the human microbiome. Thus, it is still unknown to what extent LAB-derived SMs are involved in microbiome homeostasis.
Here, we systematically investigate the biosynthetic potential of LAB from 31,977 LAB genomes, identifying 130,051 secondary metabolite biosynthetic gene clusters (BGCs) of 2,849 gene cluster families (GCFs). Most of these GCFs are species-specific or even strain-specific and uncharacterized yet. Analyzing 748 human-associated metagenomes, we gain an insight into the profile of LAB BGCs, which are highly diverse and niche-specific in the human microbiome. We discover that most LAB BGCs may encode bacteriocins with pervasive antagonistic activities predicted by machine learning models, potentially playing protective roles in the human microbiome. Class II bacteriocins, one of the most abundant and diverse LAB SMs, are particularly enriched and predominant in the vaginal microbiome. We utilized metagenomic and metatranscriptomic analyses to guide our discovery of functional class II bacteriocins. Our findings suggest that these antibacterial bacteriocins have the potential to regulate microbial communities in the vagina, thereby contributing to the maintenance of microbiome homeostasis.
Our study systematically investigates LAB biosynthetic potential and their profiles in the human microbiome, linking them to the antagonistic contributions to microbiome homeostasis via omics analysis. These discoveries of the diverse and prevalent antagonistic SMs are expected to stimulate the mechanism study of LAB's protective roles for the microbiome and host, highlighting the potential of LAB and their bacteriocins as therapeutic alternatives. Video Abstract.
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the ...request of the Editors-in-Chief.
After a thorough investigation, the Editors have concluded that the acceptance of this article was partly based upon the positive advice of one illegitimate reviewer report. The report was submitted from an email account which was provided to the journal as a suggested reviewer during the submission of the article. Although purportedly a real reviewer account, the Editors have concluded that this was not of an appropriate, independent reviewer.
This manipulation of the peer-review process represents a clear violation of the fundamentals of peer review, our publishing policies, and publishing ethics standards. Apologies are offered to the reviewer whose identity was assumed and to the readers of the journal that this deception was not detected during the submission process.
Plasmid-mediated quinolone resistance (PMQR) remains one of the main mechanisms of bacterial quinolone resistance and plays an important role in the transmission of antibiotic resistance genes ...(ARGs). In this study, two novel plasmids, p3M-2A and p3M-2B, which mediate quinolone resistance in Proteus vulgaris strain 3M (P3M) were identified. Of these, only p3M-2B appeared to be a qnrD-carrying plasmid. Both p3M-2A and p3M-2B could be transferred into Escherichia coli, and the latter caused a twofold change in ciprofloxacin resistance, according to the measured minimum inhibitory concentration (MIC). Plasmid curing/complementation and qRT-PCR results showed that p3M-2A can directly regulate the expression of qnrD in p3M-2B under treatment with ciprofloxacin, in which process, ORF1 was found to play an important role. Sequence alignments and phylogenetic analysis revealed the evolutionary relationships of all reported qnrD-carrying plasmids and showed that ORF1–4 in p3M-2B is the most conserved backbone for the normal function of qnrD-carrying plasmids. The identified direct repeats (DR) suggested that, from an evolutionary perspective, p3M-2B may have originated from the 2683-bp qnrD-carrying plasmid and may increase the possibility of plasmid recombination and then of qnrD transfer. To the best of our knowledge, this is the first identification of a novel qnrD-carrying plasmid isolated from a P. vulgaris strain of shrimp origin and a plasmid that plays a regulatory role in qnrD expression. This study also sheds new light on plasmid evolution and on the mechanism of horizontal transfer of ARGs encoded by plasmids.
Long-term trends in fog episodes, vertical variations of atmospheric boundary structure, and air pollutant concentrations during two different heavy fog events in the Tianjin area were analyzed. The ...total amount of fog has increased since 1980 due to the stability of the boundary layer and an increase of pollutant emissions. The variation in the characteristics of the boundary layer and air pollutant concentrations were significantly different between the two fog processes （fog I and fog ll）. The onset of fog I was accompanied by a temperature inversion in the low atmosphere, and the average kinetic energy showed a clear diurnal trend and vertical variation, which increased with height. The dissipation of fog I was mainly due to turbulence. However, the atmospheric stratification was not stable in the lower layer before the onset of fog If. The diurnal and vertical changes in kinetic energy were very small, in which turbulent momentum at each measurement height tended to be zero. In the dissipation process of fogⅡ, wind speed increased significantly. Surface PM2.s concentrations decreased, but the ratio of PMzs to PM10 increased from 0.66 to 0.82 until fog I dissipated. However, the concentration of PMzs did not decrease at the early stage of fog Ⅱ, but the ratio of PM2.5 to PM10 PM2.5JPM10 decreased to 0.21 when fog Ⅱ dissipated. This study showed that there was a clear difference in the evolution of pollutant concentration for different pollutants and in different developing stages during the fog events. PM2.5 concentration accumulated faster than those of SO2 and NOx, and the PM2.5 cumulative rate was greater in the mid-term of the fog process.
Aptamer-functionalized two-dimensional photonic crystal (2DPC) hydrogels are reported for the detection of adenosine (AD). As a molecular recognition group, an AD-binding aptamer was covalently ...attached to 2DPC hydrogels. This aptamer selectively and sensitively binds AD, changing the conformation of the aptamer from a long single-stranded structure (AD-free conformation) to a short hairpin loop structure (AD-bound conformation). The AD-binding-induced changes of aptamer conformation reduced the volume of the 2DPC hydrogels and decreased the interparticle spacing of the 2DPC embedded in the hydrogel network. The particle spacing changes being dependent on AD concentration were determined by measuring 2DPC light diffraction using a simple laser pointer. The 2DPC hydrogel sensor showed a large particle spacing decrease of ~ 110 nm in response to 1 mM AD in phosphate-buffered saline (PBS). The linear range of determination of AD was 0.1 nM to 1 mM and the limit of detection was 0.09 nM. The hydrogel sensor response for real samples was then validated in diluted fetal bovine serum (FBS) and human urine. The average % difference in particle spacing changes measured between diluted FBS and pure PBS was only 3.99%. In diluted human urine, the recoveries for the detection of AD were 95–101% and the relative standard deviations were 4.9–7.8%. The results demonstrate the potential applicability of the hydrogel sensor for real samples. This sensing concept, using the aptamer-functionalized 2DPC hydrogels, allows for a simple, sensitive, selective, and reversible detection of AD. It may enable sensor development for a wide variety of analytes by simply changing the aptamer recognition group.
Graphical abstract
In this paper, we investigate the content deployment problem from precaching and device-to-device communication perspectives. In the precaching stage, contents are prefetched and stored in edge nodes ...to be quickly provided to end users. In the device-to-device communication process, intermediate nodes face a dilemma in deciding whether to cache contents coming from or going to neighboring nodes to accelerate the content delivery. We call the former proactive caching and the latter reactive caching. We then design ProRec, a unified caching framework, by jointly considering the two cases with the goal of maximizing the content hit ratio. ProRec first addresses the optimization problem using the method of Lagrangian multipliers and obtains a general solution to the optimal content copies. Second, a greedy solution, proven to achieve the optimum with a probability of at least
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, is used to cache and replace contents. Finally, an edge computing simulation platform that includes real and synthetic traces is built as a case study to verify the effectiveness of ProRec. The numerical results show that it simultaneously improves the cache hit ratio and content delivery delay.
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