Genome-wide survey and expression analysis of NIN-like Protein (NLP) genes reveals its potential roles in the response to nitrate signaling in tomato

Background Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference for nitrate as an inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. Results In this study, genome-wide analysis identified six NLP members in tomato genome. These members were clustered into three clades in a phylogenetic tree. Comparative genomic analysis showed that SlNLP genes exhibited collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in the tomato genome. Tissue-specific expression analysis showed that one of the close homologs of AtNLP6/7, SlNLP3, was strongly expressed in roots during both the seedling and flowering stages, that SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves and that SlNLP6 was expressed at high levels in fruits. Furthermore, the nitrate uptake in tomato roots and the expression patterns of SlNLP genes were measured under nitrogen deficiency and nitrate resupply conditions. Four SlNLPs, SlNLP1, SlNLP2, SlNLP4 and SlNLP6, were upregulated after nitrogen starvation. And SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions These results provide significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.

Characterisitcs of Saccharomyces boulardii for reducing ammonia emission from livestock manure

Ammonia from livestock manure acts as a precursor to produce particulate matter (PM) by reacting with atmospheric chemical components volatilized from various sources. Ammonia itself acts as a toxic substance to human health, and thus has direct or indirect adverse effects on human health. This study aimed to verify the effectiveness and mechanism of action of Saccharomyces boulardii (SB) in reducing the ammonia emission from livestock manure. The specific ability of SB was confirmed through comparative verification with S. cerevisiae (SC) belonging to the same genus. SB and SC could use 50% of ammonia–nitrogen as inorganic nitrogen source in minimal medium. In the control group, the pH level of manure was significantly increased compared to the pH level at 0 h, and the DNA concentration of Proteus mirabilis, which increase the manure pH through ammonia production, was found to increase by 2.7-fold. Significant decrease in pH and proliferation of P. mirabilis was found in SB group compared to control (p < 0.05). The SB group also reduced the amount of ammonia emitted from manure by 25% for 35 days. These results suggested that SB contributed to reducing ammonia emission from manure by reducing pH and inhibiting HAB as well as removing ammonia–nitrogen. Accordingly, SB as a microbiological agent is expected to contribute not only to reduce ammonia emission but also to improve manure quality as a fertilizer.

Title: Genome-Wide Survey and Expression Analysis of NIN-Like Protein (NLP) Genes Reveals Its Potential Roles in the Response to Nutrition Deficiency in Tomato

Background: Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference of nitrate as inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-Like Proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. Results: In this study, genome-wide analysis revealed six NLP members in tomato genome. They were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that SlNLP genes had collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in tomato genome. Tissue-specific expression analysis showed that the close homologues of AtNLP6/7, SlNLP3, was strongly expressed in roots during both seedling and flowering stages; SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves; and SlNLP6 were expressed in high levels in fruits. Further, the nitrate uptake in tomato roots and expression patterns of SlNLP genes were measured under nitrogen/phosphate/potassium deficiency and nitrate resupply conditions. The transcript abundance of SlNLP3 decreased to 70% under phosphate/potassium deficiency. Most of SlNLPs were up-regulated after nitrogen starvation. SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions: These results provided significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.

An in silicodata miningof theammonium transporter gene familyin Ananas comosusL.

Arguably, nitrogen (N) is an important and essential component for plant growth and development. Ammonium is a major inorganic nitrogen source for plants mobilized by ammonium transporter (AMT) among N available sources. In this study, data mining revealed that in theAnanas comosusL. genome was identified eight AMT family genes. The eight pineapple AcoAMT proteins were identified and phylogenetically clustered into two groups with AMT proteins from other plants. Two pairs ofAcoAMT(AcoAMTaandAcoAMTg) genes located on chromosome 1 and unchromosome appear to be segmental duplications. Based on this information, we conducted a comprehensive analysis using some bioinformatics tools to characterize the identified genes individually. The comprehensive analysis of AMT will provide an essential foundation for further investigation of the regulatory mechanisms ofAcoAMTsinA. comosusL.

Agroresidues enhanced peroxidase activity expression by Bacillus sp. MABINYA-1 under submerged fermentation

Agroresidues have continued to gain preference over conventional carbon sources for microbial enzyme production due to the low price and abundance in the environment. Therefore, this study aimed at improving peroxidase yield by Bacillus sp. MABINYA-1 (BMAB-1) using agroresidues under submerged fermentation. The culture parameters that support maximum peroxidase yield by BMAB-1 was initially determined and the results showed that peroxidase activity expression was optimum at pH 5, 30 °C and 150 rpm while veratryl alcohol and ammonium sulphate served as the best peroxidase-inducer and inorganic nitrogen source, respectively. BMAB-1 exhibited maximum peroxidase expression (17.50 ± 0.10 U/mg) at 72 h using kraft lignin liquid medium (KLLM) under the optimized culture conditions. Upon utilization of selected agroresidues (sawdust, wheat straw and maize stover) as sole carbon sources by BMAB-1 in the fermentation process, peroxidase activity was significantly enhanced when compared with glucose (14.91 ± 0.31 U/mg) and kraft lignin (17.50 ± 0.10 U/mg). Sawdust produced the highest peroxidase yield (47.14 ± 0.41 U/mg), followed by maize stover (37.09 ± 0.00 U/mg) while wheat straw yielded the lowest peroxidase specific activity (21.65 ± 0.35 U/mg). This indicates that utilization of sawdust by BMAB-1 resulted in 3.2- and 2.7-fold increase in peroxidase activity expression as compared to glucose and kraft lignin, respectively. The aptitude of BMAB-1 to utilize agroresidues would reduce the cost of peroxidase production by the bacteria since the substrates are cheaper than the conventional carbon sources and are, as well, more readily available.

High-yield production and biochemical characterization of α-galactosidase produced from locally isolated Penicillium sp.

Background α-Galactosidase is widely used in various biotechnological applications such as food processing, beet sugar, the pulp and paper industries, synthesis of oligosaccharides by trans-galactosylation, hydraulic fracturing of oil and gas wells, and medical applications. Results Screening and identification of fungi for α-galactosidase activity was performed. The isolate Penicillium sp. showed good α-galactosidase activity. α-Galactosidase production by the fungal strain Penicillium sp. cultivated in solid state fermentation (SSF) conditions using copra mannan extract as nutrient medium was investigated. The maximum α-galactosidase activity of 5.391 U/mL was obtained in defatted copra meal (dFCO) as carbon source, which is 2–3% greater as compared with commercial mannans and unprocessed copra meal. The highest product yield of α-galactosidase was obtained with media containing yeast extract (6.672 U/ml) as organic nitrogen and ammonium nitrate (6.325 U/ml) and as inorganic nitrogen source with media pH 5.5, and the time course of enzyme production was at the 5th day of fermentation, respectively. The optimum pH of α-galactosidase was obtained at pH 5 and optimum temperature at 60 °C. The enzyme was stable between pH 4 and 6 and retained more than 50% of residual activity for an 8-h incubation period. The Ca+2 ions enhanced the enzyme activity and Mn+2 ions have not altered the enzyme activity, whereas Hg+2 strongly inhibited the enzyme activity. Conclusions The findings of present investigations on α-galactosidase are of particular interest for its application in the food processing industry.

Exoproduction and Molecular Characterization of Peroxidase from Ensifer adhaerens

The increased industrial application potentials of peroxidase have led to high market demand, which has outweighed the commercially available peroxidases. Hence, the need for alternative and efficient peroxidase-producers is imperative. This study reported the process parameters for enhanced exoperoxidase production by Ensifer adhaerens NWODO-2 (accession number: KX640918) for the first time, and characterized the enzyme using molecular methods. Peroxidase production by the bacteria was optimal at 48 h, with specific productivity of 12.76 U mg−1 at pH 7, 30 °C and 100 rpm in an alkali lignin fermentation medium supplemented with guaiacol as the most effective inducer and ammonium sulphate as the best inorganic nitrogen source. Upon assessment of some agricultural residues as sources of carbon for the enzyme production, sawdust gave the highest peroxidase productivity (37.50 U mg−1) under solid-state fermentation. A search of the polymerase chain reaction (PCR)-amplified peroxidase gene in UniProtKB using blastx showed 70.5% similarity to an uncharacterized protein in Ensifer adhaerens but phylogenetic analysis suggests that the gene may encode a catalase-peroxidase with an estimated molecular weight of approximately 31 kDa and isoelectric point of about 11. The nucleotide sequence of the detected gene was deposited in the GenBank under the accession number MF374336. In conclusion, the ability of the strain to utilize lignocellulosic materials for peroxidase production augurs well for biotechnological application as this would greatly reduce cost, which is a major challenge in industrial enzyme production.

Production of high cellulase yields from polypore fungi in solid-state fermentation using green tea waste

Polypores are diverse macrofungi that have been extensively studied for their enzyme production capabilities. Presently, these enzymes are being used for many industrial purposes. However, the high-cost associated with their production is the main barrier to their broader application. This work aimed to study the optimal medium and conditions by using solid state fermentation. Seven polypore strains were used for cellulase activity screening. The fermentation experiments were carried out in 250 mL Erlenmeyer flasks with green tea waste as a substrate. Notably, Microporus sp. KA038 showed the best level of activity of 81.8 IU/gds. Various parameters such as temperature on growth, moisture content, nitrogen source, initial pH value, inoculum size and incubation time were considered to determine the optimal conditions for cellulase production. The optimal medium consisted of green tea leaves as a carbon source, beef extract as an organic nitrogen source, and NH4H2PO4 as an inorganic nitrogen source, while pH 7.0 and an incubation temperature of 30°C for 4 days resulted in a high enzyme yield with Microporus sp. KA038.