Transcriptome analysis of skin color variation during and after overwintering of Malaysian red tilapia

The commercial value of red tilapia is hampered by variations in skin color during overwintering. In this study, three types of skin of red tilapia, including the skin remained pink color during and after overwintering (P), the skin changed from pink color to black color during overwintering and remained black color after overwintering (P-B), and the skin changed from pink color to black color during overwintering but recovered to pink color when the temperature rose after overwintering (P-B-P), were used to analyze their molecular mechanisms of color variation. The transcriptome results revealed that the P, P-B, and P-B-P libraries had 43, 42, and 43 million clean reads, respectively. The top 10 abundance mRNAs and specific mRNAs (specificity measure SPM > 0.9) were screened. After comparing intergroup gene expression levels, there were 2528, 1924, and 1939 differentially expressed genes (DEGs) between P-B-P and P-B, P-B-P and P, and P-B and P, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of color-related mRNAs showed that a number of DEGs, including tyrp1, tyr, pmel, mitf, mc1r, asip, tat, hpdb, and foxd3, might play a potential role in pigmentation. Additionally, the co-expression patterns of genes were detected within the pigment-related pathways by the PPI network from P-B vs. P group. Furthermore, DEGs from the apoptosis and autophagy pathways, such as baxα, beclin1, and atg7, might be involved in the fading of red tilapia melanocytes. The findings will aid in understanding the molecular mechanism underlying skin color variation in red tilapia during and after overwintering as well as lay a foundation for future research aimed at improving red tilapia skin color characteristics.

Distinct skin morphological and transcriptomic profiles between wild and albino Oscar Astronotus ocellatus

Oscar Astronotus ocellatus is an important ornamental fish, including albino and wild varieties. Albino individuals attract aquarium hobbyists due to their unique body color, but studies on the species' albinism mechanism are currently scarce. Here, we investigated the morphological and transcriptomic profiles of the skin of albino and wild Oscar. The results showed that the albino type had fewer oval-shaped melanophores and immature melanosomes but that the wild type contained more stellate-shaped melanophores and mature melanosomes. Albino Oscar had a degenerative pigment layer without obvious melanin deposition and content, while the wild type contained more concentrated melanin within the pigment layer. A total of 272,392 unigenes were detected, 109 of which were identified as differentially expressed genes (DEGs) between albino and wild Oscar. Pathways of DEGs, including those involved in complement and coagulation cascades, novobiocin biosynthesis, Th1 and Th2 cell differentiation, and tropane, piperidine and pyridine alkaloid biosynthesis, were significantly enriched. DEGs, including upregulated Sfrp5 and Tat, and downregulated Wnt-10a, Ppp3c, Notch1 and Trim27 involved in the Wnt signaling pathway, Notch signaling pathway, tyrosine metabolism, MAPK signaling pathway and melanogenesis, might be associated with the albinism of Oscar. This study characterized the difference in melanophore morphology between wild and albino Oscar and identified some albinism-related candidate genes and signaling pathways, helping to understand the genetic mechanism of fish albinism.

Comparative transcriptome analysis of molecular mechanism underlying gray-to-red body color formation in red crucian carp (Carassius auratus, red var.)

Red crucian carp (Carassius auratus red var.) is an ornamental fish with vivid red/orange color. It has been found that the adult body color of this strain forms a gray-to-red change. In this study, skin transcriptomes of red crucian carp are first obtained for three different stages of body color development, named by gray-color (GC), color-variation (CV), and red-color (RC) stages, respectively. From the skins of GC, CV, and RC, 103,229; 108,208; and 120,184 transcripts have been identified, respectively. Bioinformatics analysis reveals that 2483, 2967, and 4473 unigenes are differentially expressed between CV and GC, RC and CV, and RC and GC, respectively. A part of the differentially expressed genes (DEGs) are involved in the signaling pathway of pigment synthesis, such as the melanogenesis genes (Mitfa, Pax3a, Foxd3, Mc1r, Asip); tyrosine metabolism genes (Tyr, Dct, Tyrp1, Silva, Tat, Hpda); and pteridine metabolism genes (Gch, Xdh, Ptps, Tc). According to the data of transcriptome and quantitative PCR, the expression of Mitfa and its regulated genes which include the genes of Tyr, Tyrp1, Dct, Tfe3a, and Baxα, decreases with gray-to-red change. It is suggested that Mitfa and some genes, being related to melanin synthesis or melanophore development, are closely related to the gray-to-red body color transformation in the red crucian carp. Furthermore, the DEGs of cell apoptosis and autophagy pathway, such as Tfe3a, Baxα, Hsp70, Beclin1, Lc3, Atg9a, and Atg4a, might be involved in the melanocytes fade away of juvenile fish. These results shed light on the regulation mechanism of gray-to-red body color transformation in red crucian carp, and are helpful to the selective breeding of ornamental fish strains.

FkbN and Tcs7 are pathway-specific regulators of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis L19

FK506 (tacrolimus), which is produced by many Streptomyces strains, is clinically used as an immunosuppressive agent and for treatment of inflammatory skin diseases. Here, we identified that the FK506 biosynthetic gene cluster in an industrial FK506-producing strain Streptomyces tsukubaensis L19 is organized as eight transcription units. Two pathway-specific regulators, FkbN and Tcs7, involved in FK506 biosynthesis from S. tsukubaensis L19 were characterized in vivo and in vitro. FkbN activates the transcription of six transcription units in FK506 biosynthetic gene cluster, and Tcs7 activates the transcription of fkbN. In addition, the DNA-binding specificity of FkbN was determined. Finally, a high FK506-producing strain was constructed by overexpression of both fkbN and tcs7 in S. tsukubaensis L19, which improved FK506 production by 89 % compared to the parental strain.

Genetic Determinants for Pyomelanin Production and Its Protective Effect against Oxidative Stress in Ralstonia solanacearum

Ralstonia solanacearum is a soil-borne plant pathogen that infects more than 200 plant species. Its broad host range and long-term survival under different environmental stress conditions suggest that it uses a variety of mechanisms to protect itself against various types of biotic and abiotic stress. R. solanacearum produces a melanin-like brown pigment in the stationary phase when grown in minimal medium containing tyrosine. To gain deeper insight into the genetic determinants involved in melanin production, transposon-inserted mutants of R. solanacearum strain SL341 were screened for strains with defective melanin-producing capability. In addition to one mutant already known to be involved in pyomelanin production (viz., strain SL341D, with disruption of the hydroxphenylpyruvate dioxygenase gene), we identified three other mutants with disruption in the regulatory genes rpoS, hrpG, and oxyR, respectively. Wild-type SL341 produced pyomelanin in minimal medium containing tyrosine whereas the mutant strains did not. Likewise, homogentisate, a major precursor of pyomelanin, was detected in the culture filtrate of the wild-type strain but not in those of the mutant strains. A gene encoding hydroxyphenylpyruvate dioxygenase exhibited a significant high expression in wild type SL341 compared to other mutant strains, suggesting that pyomelanin production is regulated by three different regulatory proteins. However, analysis of the gene encoding homogentisate dioxygenase revealed no significant difference in its relative expression over time in the wild-type SL341 and mutant strains, except for SL341D, at 72 h incubation. The pigmented SL341 strain also exhibited a high tolerance to hydrogen peroxide stress compared with the non-pigmented SL341D strain. Our study suggests that pyomelanin production is controlled by several regulatory factors in R. solanacearum to confer protection under oxidative stress.

An overview on transcriptional regulators in Streptomyces

Streptomyces are Gram-positive microorganisms able to adapt and respond to different environmental conditions. It is the largest genus of Actinobacteria comprising over 900 species. During their lifetime, these microorganisms are able to differentiate, produce aerial mycelia and secondary metabolites. All of these processes are controlled by subtle and precise regulatory systems. Regulation at the transcriptional initiation level is probably the most common for metabolic adaptation in bacteria. In this mechanism, the major players are proteins named transcription factors (TFs), capable of binding DNA in order to repress or activate the transcription of specific genes. Some of the TFs exert their action just like activators or repressors, whereas others can function in both manners, depending on the target promoter. Generally, TFs achieve their effects by using one- or two-component systems, linking a specific type of environmental stimulus to a transcriptional response. After DNA sequencing, many streptomycetes have been found to have chromosomes ranging between 6 and 12Mb in size, with high GC content (around 70%). They encode for approximately 7000 to 10,000 genes, 50 to 100 pseudogenes and a large set (around 12% of the total chromosome) of regulatory genes, organized in networks, controlling gene expression in these bacteria. Among the sequenced streptomycetes reported up to now, the number of transcription factors ranges from 471 to 1101. Among these, 315 to 691 correspond to transcriptional regulators and 31 to 76 are sigma factors. The aim of this work is to give a state of the art overview on transcription factors in the genus Streptomyces.

Towards a new science of secondary metabolism

Secondary metabolites are a reliable and very important source of medicinal compounds. While these molecules have been mined extensively, genome sequencing has suggested that there is a great deal of chemical diversity and bioactivity that remains to be discovered and characterized. A central challenge to the field is that many of the novel or poorly understood molecules are expressed at low levels in the laboratory-such molecules are often described as the 'cryptic' secondary metabolites. In this review, we will discuss evidence that research in this field has provided us with sufficient knowledge and tools to express and purify any secondary metabolite of interest. We will describe 'unselective' strategies that bring about global changes in secondary metabolite output as well as 'selective' strategies where a specific biosynthetic gene cluster of interest is manipulated to enhance the yield of a single product.

A putative ABC transporter, hatABCDE, is among molecular determinants of pyomelanin production in Pseudomonas aeruginosa

Pyomelanin overproduction is a common phenotype among Pseudomonas aeruginosa isolates recovered from cystic fibrosis and urinary tract infections. Its prevalence suggests that it contributes to the persistence of the producing microbial community, yet little is known about the mechanisms of its production. Using transposon mutagenesis, we identified factors that contribute to melanogenesis in a clinical isolate of P. aeruginosa. In addition to two enzymes already known to be involved in its biosynthesis (homogentisate dioxygenase and hydroxyphenylpyruvate dioxygenase), we identified 26 genes that encode regulatory, metabolic, transport, and hypothetical proteins that contribute to the production of homogentisic acid (HGA), the monomeric precursor of pyomelanin. One of these, PA14_57880, was independently identified four times and is predicted to encode the ATP-binding cassette of an ABC transporter homologous to proteins in Pseudomonas putida responsible for the extrusion of organic solvents from the cytosol. Quantification of HGA production by P. aeruginosa PA14 strains missing the predicted subcomponents of this transporter confirmed its role in HGA production: mutants unable to produce the ATP-binding cassette (PA14_57880) or the permease (PA14_57870) produced substantially less extracellular HGA after growth for 20 h than the parental strain. In these mutants, concurrent accumulation of intracellular HGA was observed. In addition, quantitative real-time PCR revealed that intracellular accumulation of HGA elicits upregulation of these transport genes. Based on their involvement in homogentisic acid transport, we rename the genes of this operon hatABCDE.

Identification of mutants with altered phenazine production in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that causes serious and chronic infections. Many secondary metabolites are secreted throughout its growth, among which phenazine is a known virulence factor and signalling molecule. Phenazine is coordinately controlled by the global regulatory quorum-sensing (QS) systems. Despite the detailed understanding of phenazine biosynthesis pathways in P. aeruginosa, the regulatory networks are still not fully clear. In the present study, the regulation of the phzA1B1C1D1E1F1G1 operon (phzA1) has been investigated. Screening of 5000 transposon mutants revealed 14 interrupted genes with altered phzA1 expression, including PA2593 (QteE), which has been identified as a novel regulator of the QS system. Overexpression of qteE in P. aeruginosa significantly reduced the accumulation of homoserine lactone signals and affected the QS-controlled phenotypes such as the production of pyocyanin, rhamnolipids and LasA protease and swarming motility. Indeed, overexpression of qteE in P. aeruginosa attenuated its pathogenicity in the potato and fruit fly infection models. These findings suggest that qteE plays an important role in P. aeruginosa pathogenicity and is part of the regulatory networks controlling phenazine production.

Reciprocal regulation between SigK and differentiation programs in Streptomyces coelicolor

Here we reported that deletion of SigK (SCO6520), a sigma factor in Streptomyces coelicolor, caused an earlier switch from vegetative mycelia to aerial mycelia and higher expression of chpE and chpH than that in the wild type. Loss of SigK also resulted in accelerated and enhanced production of antibiotics, actinorhodin, and undecylprodigiosin and increased expression of actII-orf4 and redD. These results suggested that SigK had a negative role in morphological transition and secondary metabolism. Furthermore, the sigK promoter (sigKp) activity gradually increased and sigK expression was partially dependent on SigK, but this dependence decreased during the developmental course of substrate mycelia. Meanwhile, two potentially nonspecific cleavages occurred between SigK and green fluorescent protein, and the SigK fusion proteins expressed under the constitutive promoter ermEp* sharply decreased and disappeared when aerial mycelia emerged. If expressed under sigKp, 3FLAG-SigK showed similar dynamic patterns but did not decrease as sharply as SigK expressed under ermEp*. These data suggested that the climbing expression of sigK might reduce the prompt degradation of SigK during vegetative hypha development for the proper timing of morphogenesis and that SigK vanished to remove the block for the emergence of aerial mycelia. Thus, we proposed that SigK had inhibitory roles on developmental events and that these inhibitory effects may be released by SigK degradation.