The ease of genetic manipulation, low cost, rapid growth and number of previous studies have made Escherichia coli one of the most widely used microorganism species for producing recombinant ...proteins. In this post-genomic era, challenges remain to rapidly express and purify large numbers of proteins for academic and commercial purposes in a high-throughput manner. In this review, we describe several state-of-the-art approaches that are suitable for the cloning, expression and purification, conducted in parallel, of numerous molecules, and we discuss recent progress related to soluble protein expression, mRNA folding, fusion tags, post-translational modification and production of membrane proteins. Moreover, we address the ongoing efforts to overcome various challenges faced in protein expression in E. coli, which could lead to an improvement of the current system from trial and error to a predictable and rational design.
The liver, being closely connected to the gut via the hepatic portal vein, is the first recipient of gut microbiome metabolites and antigens, including bile acids (BAs), lipopolysaccharide (LPS), ...choline, indole derivatives, and short-chain fatty acids 7. Clostridium species in the gut microbiome produce secondary BAs by 7α-dehydroxylation In the gut, bacteria from Clostridium cluster XIVa (including Clostridium scindens, C. hiranonis, and C. hylemonae) and Clostridium cluster XI (C. sordellii) can convert the primary 7α-hydroxyl BAs, cholic acid (CA), and chenodeoxycholic acid (CDCA), into the secondary BAs deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, through a 7α/β-dehydroxylation reaction catalyzed by enzymes encoded by the BA-inducible (bai) operon 25. ...BaiN reduces the intermediates to form DCA or LCA, which are secreted from the bacterial cell and therefore released into the host intestine 28. BA, bile acid; CA, cholic acid; CDCA, chenodeoxycholic acid; COX2, cyclooxygenase 2; CXCL16, chemokine (C-X-C motif) ligand 16; CXCR6, C-X-C chemokine receptor type 6; DCA, deoxycholic acid; GLCA, glucuronic acid; HCA, hyocholic acid; HDCA, hyodeoxycholic acid; LCA, lithocholic acid; LTA, lipoteichoic acid; MCA, muricholic acid; MDCA, murideoxycholic acid; PGE2, prostaglandin E2; PTGER4, prostaglandin E receptor 4; UDCA, ursodeoxycholic acid. https://doi.org/10.1371/journal.ppat.1007954.g001 Secondary BAs regulate liver cancer via NKT cells Ma and colleagues demonstrated that primary and secondary BAs additionally mediate the opposing effects on liver tumor growth through NKT cells (Fig 1) 10.
Bile acid metabolism by the gut microbiome exerts both beneficial and harmful effects on host health. Microbial bile salt hydrolases (BSHs), which initiate bile acid metabolism, exhibit both positive ...and negative effects on host physiology. In this study, 5,790 BSH homologs were collected and classified into seven clusters based on a sequence similarity network. Next, the abundance and distribution of BSH in 380 metagenomes from healthy participants were analyzed. It was observed that different clusters occupied diverse ecological niches in the human microbiome and that the clusters with signal peptides were relatively abundant in the gut. Then, the association between BSH clusters and 12 human diseases was analyzed by comparing the abundances of BSH genes in patients (n = 1,605) and healthy controls (n = 1,540). The analysis identified a significant association between BSH gene abundance and 10 human diseases, including gastrointestinal diseases, obesity, type 2 diabetes, liver diseases, cardiovascular diseases, and neurological diseases. The associations were further validated by separate cohorts with inflammatory bowel diseases and colorectal cancer. These large-scale studies of enzyme sequences combined with metagenomic data provide a reproducible assessment of the association between gut BSHs and human diseases. This information can contribute to future diagnostic and therapeutic applications of BSH-active bacteria for improving human health.
The metabolism of bile acid by the gut microbiota is associated with host health. Bile salt hydrolases (BSHs) play a crucial role in controlling microbial bile acid metabolism. Herein, we conducted a ...comparative study to investigate the alterations in the abundance of BSHs using data from three human studies involving dietary interventions, which included a ketogenetic diet (KD) versus baseline diet (BD), overfeeding diet (OFD) versus underfeeding diet, and low-carbohydrate diet (LCD) versus BD. The KD increased BSH abundance compared to the BD, while the OFD and LCD did not change the total abundance of BSHs in the human gut. BSHs can be classified into seven clusters; Clusters 1 to 4 are relatively abundant in the gut. In the KD cohort, the levels of BSHs from Clusters 1, 3, and 4 increased significantly, whereas there was no notable change in the levels of BSHs from the clusters in the OFD and LCD cohorts. Taxonomic studies showed that members of the phyla Bacteroidetes, Firmicutes, and Actinobacteria predominantly produced BSHs. The KD altered the community structure of BSH-active bacteria, causing an increase in the abundance of Bacteroidetes and decrease in Actinobacteria. In contrast, the abundance of BSH-active Bacteroidetes decreased in the OFD cohort, and no significant change was observed in the LCD cohort. These results highlight that dietary patterns are associated with the abundance of BSHs and community structure of BSH-active bacteria and demonstrate the possibility of manipulating the composition of BSHs in the gut through dietary interventions to impact human health.
The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily in Metazoa is responsible for protein modification, nucleic acid repair and/or modification, and fatty acid metabolism.
...Phylogenetic analysis, protein sequence similarity network (SSN) and other bioinformatics tools were used to analyze the evolutionary relationship and make functional inferences of Metazoa 2OG oxygenases.
Sixty-four 2OG oxygenases have been previously found in Homo sapiens; they catalyze two reactions: hydroxylation and demethylation. Phylogenetic analyses indicated that enzymes with similar domain architecture are always clustered together, and the redox function can be performed by the 2OG oxygenase domain or Jumonji C (JmjC) domain, where the JmjC domain is always fused to other functional domains. We used the SSN to make functional inferences and to conduct distribution analysis of Metazoa 2OG oxygenases. >11,000 putative 2OG oxygenases across Metazoa could be assigned potential functions based on the SSN. The multiple sequence alignments showed that the residues binding iron are most highly conserved in both the 2OG oxygenase domain and JmjC domain. In contrast, the residues binding oxoglutarate are quite different in the two domains: the 2OG oxygenase domain tends to have an Arg/Lys at the C terminus, whereas the JmjC domain, an Asn/Lys residue in the middle region.
The results indicated that gene duplication and vertical gene transfer have played important roles in 2OG oxygenase evolution in Metazoa and clarified the difference between the 2OG oxygenase domain and JmjC domain.
These findings expand the understanding of the diversity, evolution, and functions of 2OG oxygenases.
•2OG oxygenases in humans catalyze two reactions: hydroxylation and demethylation.•>11,000 putative 2OG oxygenases across Metazoa could be assigned potential functions.•Gene duplication and vertical gene transfer have played important roles in 2OG oxygenase evolution in Metazoa.•The redox functions of the enzymes are performed by the 2OG oxygenase domain or JmjC domain.•The residues binding oxoglutarate are quite different in the two domains.
Prodigiosin is a red pigment produced by
with anticancer, antimalarial, and antibacterial effects. In this study, we extracted and identified a red pigment from a culture of
strain ZPG19 and ...investigated its effect on the growth performance and intestinal microbiota of Kunming mice. High-performance liquid chromatography/mass spectrometry revealed that the pigment had a mass-to-charge ratio (
/
) of 324.2160, and thus it was identified as prodigiosin. To investigate the effect of prodigiosin on the intestinal microbiota, mice (n = 5) were administered 150 μg/kg/d prodigiosin (crude extract, 95% purity) via the drinking water for 18 days. Administration of prodigiosin did not cause toxicity in mice. High-throughput sequencing analysis revealed that prodigiosin altered the cecum microbiota abundance and diversity; the relative abundance of
significantly decreased, whereas
significantly increased. This finding indicates that oral administration of prodigiosin has a beneficial effect on the intestinal microbiota of mice. As prodigiosin is non-toxic to mouse internal organs and improves the mouse intestinal microbiota, we suggest that it is a promising candidate drug to treat intestinal inflammation.
, a moderately halophilic bacterium, accumulates a variety of compatible solutes including glycine betaine, glutamate, glutamine, proline, and ectoine to cope with osmotic stress. Non-targeted ...analysis of intracellular organic compounds using
H-NMR showed that a large amount of trans-4-hydroxy-L-proline (Hyp), which has not been reported as a compatible solute in
, was accumulated in response to high NaCl salinity, suggesting that Hyp may be an important compatible solute in
. Candidate genes encoding proline 4-hydroxylase (PH-4), which hydroxylates L-proline to generate Hyp, were retrieved from the genome of
through domain searches based on the sequences of known PH-4 proteins. A gene, HBHAL_RS11735, which was annotated as a multidrug DMT transporter permease in GenBank, was identified as the PH-4 gene through protein expression analysis in
. The PH-4 gene constituted a transcriptional unit with a promoter and a rho-independent terminator, and it was distantly located from the proline biosynthetic gene cluster (
operon). Transcriptional analysis showed that PH-4 gene expression was NaCl concentration-dependent, and was specifically induced by chloride anion, similar to the
operon. Accumulation of intracellular Hyp was also observed in other bacteria, suggesting that Hyp may be a widespread compatible solute in halophilic and halotolerant bacteria.
As a special type of noncoding RNA, circular RNAs (circRNAs) are prevalent in many organisms. They can serve as sponges for microRNAs and protein scaffolds, or templates for protein translation, ...making them linked to cellular homeostasis and disease progression. In recent years, circRNAs have been found to be abnormally expressed during the processes of viral infection and pathogenesis, and can help a virus escape the immune response of a host. Thus, they are now considered to play important functions in the invasion and development of viruses. Moreover, the potential application of circRNAs as biomarkers of viral infection or candidates for therapeutic targeting deserves consideration. This review summarizes circRNAs in the transcriptome, including their classification, production, functions, and value as biomarkers. This review paper also describes research progress on circRNAs in viral infection (mainly hepatitis B virus, HIV, and some human herpes viruses) and aims to provide new ideas for antiviral therapies targeting circRNAs.
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