Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less ...studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.
Summary
Chlorophyll degradation naturally occurs during plant senescence. However, in fruit such as citrus, it is a positive characteristic, as degreening is an important colour development ...contributing to fruit quality. In the present work, Citrus sinensis Osbeck, cv. Newhall fruit was used as a model for chlorophyll degradation. An ethylene response factor, CitERF13, was isolated and its transcriptional changes were closely correlated with fruit peel degreening during development or in response to ethylene. Dual‐luciferase and yeast one‐hybrid assays, as well as motif mutation, indicated that CitERF13 directly binds to the CitPPH promoter and enhances its activity. Transient and stable over‐expression of CitERF13 resulted in rapid chlorophyll degradation in Nicotiana tabacum leaves and led to accumulation of pheophorbide (Pheide) a, a metabolite of pheophorbide hydrolase (PPH). Similar results were observed from transient transformation of CitERF13 in citrus fruit peel. Moreover, this function of CitERF13 was conserved within Arabidopsis and tomato, as the homologs AtERF17 and SlERF16 similarly acted as activators of PPH genes and accelerators of chlorophyll degradation.
Significance Statement
Chlorophyll degradation in the fruit is a desired trait in citrus, so understanding the underlying molecular mechanisms is important for citrus breeding. Here we show that an ethylene response factor directly binds to the promoter of PPH, a gene encoding pheohorbide hydrolase, a key mark of chlorophyll degradation.
Alginate is a linear polysaccharide produced mainly by brown algae in marine environments. Alginate consists of a linear block copolymer made up of two monomeric units, β-d-mannuronate (M) and its ...C-5 epimer α-l-guluronate (G). Alginate lyases are polysaccharide lyases (PL) that degrade alginate via a β-elimination reaction. These enzymes play an important role in marine carbon recycling and also have widespread industrial applications. So far, more than 1,774 alginate lyase sequences have been identified and are distributed into 7 PL families. In this review, the folds, conformational changes during catalysis, and catalytic mechanisms of alginate lyases are described. Thus far, structures for 15 alginate lyases have been solved and are divided into 3 fold classes: the β-jelly roll class (PL7, -14, and -18), the (α/α)n toroid class (PL5, -15, and -17), and the β-helix fold (PL6). These enzymes adopt two different mechanisms for catalysis, and three kinds of conformational changes occur during this process. Moreover, common features in the structures, conformational changes, and catalytic mechanisms are summarized, providing a comprehensive understanding on alginate lyases.
Summary
In Streptomyces, GlnR is an activator protein that activates nitrogen‐assimilation genes under nitrogen‐limiting conditions. However, less is known regarding the regulation of these genes ...under nitrogen‐rich conditions. We determined that the developmental regulator MtrA represses nitrogen‐assimilation genes in nitrogen‐rich media and that it competes with GlnR for binding to GlnR boxes. The GlnR boxes upstream of multiple nitrogen genes, such as amtB, were confirmed as MtrA binding sites in vitro by electrophoretic mobility shift assays and in vivo by ChIP‐qPCR analysis. Transcriptional analysis indicated that, on nutrient‐rich medium, MtrA profoundly repressed expression of nitrogen‐associated genes, indicating opposing roles for MtrA and GlnR in the control of nitrogen metabolism. Using in vitro and in vivo analysis, we also showed that glnR is itself a direct target of MtrA and that MtrA represses glnR transcription. We further demonstrated functional conservation of MtrA homologues in the recognition of GlnR boxes upstream of nitrogen genes from different actinobacterial species. As mtrA and glnR are widespread among actinomycetes, this mechanism of potential competitive control over nitrogen metabolism genes may be common in this group, adding a major new layer of complexity to the known regulatory network for nitrogen metabolism in Streptomyces and related species.
MtrA represses nitrogen genes in Streptomyces under nutrient‐rich conditions, whereas GlnR activates the nitrogen genes under nutrient‐poor conditions, with both proteins exerting regulation by binding GlnR boxes upstream of the nitrogen genes.
Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain ...CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean.
Aims
Aboveground litter inputs have been modified by global changes in plantation forests, where understory management is also prevalent, which may alter soil fertility and stand productivity. This ...study aimed to quantify the specific roles of litter and understory in affecting soil carbon (C) and nitrogen (N) dynamics.
Methods
A field experiment was established with four treatments, namely, litter addition (LA), understory removal (UR), litter addition and understory removal (LA + UR), and a control, in a subtropical
Cunninghamia lanceolata
plantation. Topsoil δ
13
C, organic C concentration, storage and decomposition, mineral N, N mineralization, and C and N hydrolase activities were analyzed.
Results
Litter addition significantly increased soil organic C, macro-particulate organic C (macro-POC) and mineral N at a 0–5 cm depth, but decreased δ
13
C
macro-POC
at 0–5 cm and 5–10 cm depths. Understory removal significantly increased soil NH
4
+
-N, the rates of nitrification and net N mineralization as well as the soil organic C respiration rate at the two depths, while it decreased the C storage in bulk soil, especially in mineral protected pools. The activities of β-glucosidase and β-N-acetylglucosaminidase increased with litter addition and understory removal, respectively.
Conclusions
Litter addition tends to improve soil C quantity and quality due to fresh organic C inputs, while understory removal helps increase the N supply via the acceleration of N mineralization and the absence of understory plant uptake.
Bacterial collagenolytic proteases are important because of their essential role in global collagen degradation and because of their virulence in some human bacterial infections. Bacterial ...collagenolytic proteases include some metalloproteases of the M9 family from Clostridium or Vibrio strains, some serine proteases distributed in the S1, S8, and S53 families, and members of the U32 family. In recent years, there has been remarkable progress in discovering new bacterial collagenolytic proteases and in investigating the collagen-degrading mechanisms of bacterial collagenolytic proteases. This review provides comprehensive insight into bacterial collagenolytic proteases, especially focusing on the structures and collagen-degrading mechanisms of representative bacterial collagenolytic proteases in each family. The roles of bacterial collagenolytic proteases in human diseases and global nitrogen cycling, together with the biotechnological and medical applications for these proteases, are also briefly discussed.
The type 2 diabetes mellitus (T2DM) is an urgent global health problem. T2DM patients are in a state of high oxidative stress and inflammation. Vitamin D and glutathione (GSH) play crucial roles in ...antioxidation and anti‐inflammation. However, T2DM patients have lower vitamin D and GSH levels than healthy persons. A randomized controlled trial was conducted to see the effect of the vitamin D supplementation on oxidative stress and inflammatory factors in T2DM patients. In this study, a total of 178 T2DM patients were randomly enrolled, 92 patients received regular treatment (T2DM group) and 86 patients in Vitamin D group received extra vitamin D 400 IU per day in addition to regular treatment. Serum vitamin D, GSH, GSH metabolic enzyme GCLC and GR, inflammatory factor MCP‐1, and IL‐8 levels were investigated. We found that the T2DM group has significantly higher concentrations of MCP‐1 and IL‐8 than those in the healthy donor group. After vitamin D supplementation for 90 days, T2DM patients had a 2‐fold increase of GSH levels, from 2.72 ± 0.84 to 5.76 ± 3.19 μmol/ml, the concentration of MCP‐1 decreased from 51.11 ± 20.86 to 25.42 ± 13.06 pg/ml, and IL‐8 also decreased from 38.21 ± 21.76 to 16.05 ± 8.99 pg/ml. In conclusion, our study demonstrated that vitamin D could regulate the production of GSH, thereby reducing the serum levels of MCP‐1 and IL‐8, alleviating oxidative stress and inflammation, providing evidence of the necessity and feasibility of adjuvant vitamin D treatment among patients with T2DM. On the other hand, vitamin D and GSH levels have important diagnostic and prognostic values in T2DM patients.
Diagram for randomized design of this study. In order to investigate of the correlation between vitamin D supplementation and serum glutathione levels of T2DM patients, a randomized controlled trial was conducted. A total of 178 T2DM patients were randomized to receive either vitamin D 400 IU per day or not. Healthy donors were also included in this study. Serum vitamin D, GSH, glutamate cysteine ligase (GCLC), glutathione reductase (GR), mononucleosis protein1 (MCP‐1), and leukocyte interleukin‐8 (IL‐8) levels of all three groups were investigated.
The continuous increase of nitrogen (N) deposition may exacerbate phosphorus (P) deficiency, which affects soil organic carbon (SOC) decomposition by changing microbial community characteristics in ...subtropical forests with highly weathered soils. However, there is currently little information about the role of P and the N × P interaction in SOC dynamics. Here, a field nutrient manipulation experiment was established in a subtropical plantation forest in China. Soils collected from simulated N deposition and P addition treatments for 5 years were incubated at 25 °C for 130 days. Soil microbial composition was measured using the phospholipid fatty acid method and the enzyme activities related to SOC hydrolysis were measured. The SOC concentration and δ13C in bulk soil and three particle-size fracfractions were also determined. The cumulative CO2 respired over 9 days, representing the utilization of carbon sources under field conditions, increased with N deposition levels under the without-P treatment, while no significant differences were found among the three N deposition levels in the with-P treatment. Meanwhile, P addition generally suppressed the SOC decomposition during 130 days incubation. Similarly, P addition decreased the potential organic carbon decomposition (C0) and C0/SOC ratio. In contrast, C0 increased with N deposition in the without-P treatment, while was unaffected by N deposition under the with-P treatment, suggesting the response of SOC decomposition to N deposition was affected following P addition by alteration of SOC quality. Moreover, N deposition tended to deplete the δ13C of the SOC and P addition enriched the δ13C of the macro-particulate organic carbon. Addition of P increased total microbial, fungal and bacterial biomass values by 41.6%, 90.0% and 46.9%, respectively, whereas N deposition had no significant effect. Soil fungi/bacteria ratio significantly increased by N deposition and P addition, which partly explained the reduction of SOC decomposition after P addition. The cellobioside activity significantly decreased by 48.3% after P addition, while cellobioside and β-xylosidase activities increased with N deposition, suggesting that N deposition and P addition had opposite roles in the SOC stability. These results indicate that the positive effect of N deposition on SOC decomposition was suppressed when P was added by changing microbial community and enzyme activity and enhanced P availability may result in increased SOC accumulation under N deposition scenarios in subtropical forests.
•P addition counteracted the stimulatory effect of N deposition on SOC decomposition.•P addition generally inhibited soil organic carbon (SOC) decomposition.•N deposition depleted the δ13CSOC while P addition enriched the δ13Cmacro-POC.•P addition increased total microbial biomass and fungi/bacteria ratio.•The cellobioside activity decreased with P addition but increased with N deposition.
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