Transcriptomic response of an Antarctic yeast Rhodotorula sp. USM-PSY62 to temperature changes

Aims@#Rhodotorula sp. (USM-PSY62) is a psychrophilic yeast isolated from Antarctic sea ice that grows optimally at 15°C. The inevitable global warming poses many challenges to the microbial community in Antarctica. Therefore, this studywas conceptualized to observe how USM-PSY62 adapted to fluctuations in temperature.@*Methodology and results @#Rhodotorula sp. (USM-PSY62) was grown in YPD broth until the mid-log phase. Then, the culture was transferred to four different temperatures, specifically at 0 °C, 5 °C, 15 °C and 21 °C for 24 h. Then, the RNA was extracted, sequenced and analysed. During cold adaptation, an elevated transcription of the CorA magnesium transporter gene in USM-PSY62 indicated a higher requirement for magnesium ions to gain additional enzyme cofactors or maintain cytoplasmic fluidity. The HepA homologue coding for DNA/RNA helicase was also over-expressed with log fold change 2.89 in cold conditions possibly to reorganize secondary structures of DNA and RNA. An up-regulation of the catalase gene was also observed, reflecting an increment in the concentration of reactive oxygen species and fluctuations in the associated antioxidant system. The YOP1 gene, which encodes a membrane protein associated with protein transport and membrane traffic, was the most down-regulated, with log2 fold change values of -6.93 lower under cold shock conditions. The genes responsible for the structural maintenance of chromosome (SMC) have a -8.80 in expression log2 fold change, indicating the gene was down-regulated when the temperature was shifted to 0 °C. Upon cold shock, the gene for heat shock factor protein 1 (HSF1) was also down-regulated with a log2 fold change value of - 5.86. Hsf1 is a transcriptional regulator which regulates the heat shock responses.@*Conclusion, significance and impact of study: @#In conclusion, the transcriptomic responses demonstrated by Rhodotorula sp. USM-PSY62 characterized critical physiological and biochemical compensatory mechanisms especially cellular processes and signalling, information storage and processing, and metabolism to survive at low and high temperatures. This study provides valuable data for industry, especially in the usage of molecular chaperones.

Evolution and Functional Diversity of Microbial Cold Shock Proteins / 中国生物化学与分子生物学报

Cold shock proteins (CSPs) are highly conserved in structure and diversified in function. Due to the high homology of proteins, the CSP family mostly has a fixed spherical structure. CSPs are mostly the molecular chaperons of nucleic acid, so as to regulate the transcription and translation of genes, so that the cells can recover normal growth and reproduction under adverse environmental conditions. At present, many studies have shown that although CSPs share a high degree of homology, CSPs develop functional diversity to fight against a variety of stress after natural selection under different environmental conditions. For example, CSPC protein can inhibit the expression of related proteins in the type III secretory system, and CSPD protein is mainly suitable for regulating the growth and development of nutrient-deficient cells, while the functions of CSPH and CSPF proteins remain unclear. At first, this paper summarized the details of the high homology and the diversity between CSPs family members. Secondly, the phylogenetic tree for the genetic distance between different CSPs was analyzed. The functional diversity of the family and their mechanisms in transcription and translation levels were also summarized. Finally, the existing problems of the CSP family research and their application in agriculture, food and medical fields are reviewed.

Orthogonal assays for the identification of inhibitors of the single-stranded nucleic acid binding protein YB-1

We have previously shown that high expression of the nucleic acid binding factor YB-1 is strongly associated with poor prognosis in a variety of cancer types. The 3-dimensional protein structure of YB-1 has yet to be determined and its role in transcriptional regulation remains elusive. Drug targeting of transcription factors is often thought to be difficult and there are very few published high-throughput screening approaches. YB-1 predominantly binds to single-stranded nucleic acids, adding further difficulty to drug discovery. Therefore, we have developed two novel screening assays to detect compounds that interfere with the transcriptional activation properties of YB-1, both of which may be generalizable to screen for inhibitors of other nucleic acid binding molecules. The first approach is a cell-based luciferase reporter gene assay that measures the level of activation of a fragment of the promoter by YB-1. The second approach is a novel application of the AlphaScreen system, to detect interference of YB-1 interaction with a single-stranded DNA binding site. These complementary assays examine YB-1 binding to two discrete nucleic acid sequences using two different luminescent signal outputs and were employed sequentially to screen 7360 small molecule compounds leading to the identification of three putative YB-1 inhibitors.

CspB of an arctic bacterium, Polaribacter irgensii KOPRI 22228, confers extraordinary freeze-tolerance

ABSTRACT Freezing temperatures are a major challenge for life at the poles. Decreased membrane fluidity, uninvited secondary structure formation in nucleic acids, and protein cold-denaturation all occur at cold temperatures. Organisms adapted to polar regions possess distinct mechanisms that enable them to survive in extremely cold environments. Among the cold-induced proteins, cold shock protein (Csp) family proteins are the most prominent. A gene coding for a Csp-family protein, cspB, was cloned from an arctic bacterium, Polaribacter irgensii KOPRI 22228, and overexpression of cspB greatly increased the freeze-survival rates of Escherichia coli hosts, to a greater level than any previously reported Csp. It also suppressed the cold-sensitivity of an E. coli csp-quadruple deletion strain, BX04. Sequence analysis showed that this protein consists of a unique domain at its N-terminal end and a well conserved cold shock domain at its C-terminal end. The most common mechanism of Csp function in cold adaption is melting of the secondary structures in RNA and DNA molecules, thus facilitating transcription and translation at low temperatures. P. irgensii CspB bound to oligo(dT)-cellulose resins, suggesting single-stranded nucleic acid-binding activity. The unprecedented level of freeze-tolerance conferred by P. irgensii CspB suggests a crucial role for this protein in survival in polar environments.

Mast cells promote the beiging of white adipose tissue from cold shock / 中华内分泌代谢杂志

This article is the translation of Mast Cells Promote Seasonal White Adipose Beiging in Humans, published in the Diabetes in May, 2017(Diabetes 2017,66:1237-1246), with the consent of Diabetes.This study mainly investigated the mechanism of the beiging of white adipose tissue(WAT).Studies in rodents suggested that cold shock and a number of immune mediators were important for the beiging of subcutaneous white adipose tissue (SC-WAT).This study observed the seasonal beiging of SC-WAT from lean humans, measured the gene expression of various immune cell markers, and performed multivariate analysis of the gene expression data to identify genes that could predict uncoupling protein-1(UCP-1) expression.The mechanism of the induction of UCP-1 from adipocytes by mast cells was also explored by in vitro experiment.The results showed that TIB64 mast cells responded to cold shock by releasing histamine and interleukin 4 (IL-4) which promoted the expression of UCP-1 and the lipolysis of 3T3-L1 adipocytes.Pharmacological block of the degranulation of mast cells potently inhibited the release of histamine and adipocyte UCP-1 mRNA induction by conditioned medium.In summary, mast cells are an important immune cell type in the beiging of WAT which sense colder temperatures, and release factors that promote UCP-1 expression.

Physiological stress responses in the warm-water fish matrinxã (Brycon amazonicus ) subjected to a sudden cold shock / Respostas fisiológicas ao estresse do peixe de águas tépidas matrinxã (Brycon amazonicus ) submetido à queda brusca de temperatura

The present work evaluated several aspects of the generalized stress response [endocrine (cortisol), metabolic (glucose), hematologic (hematocrit and hemoglobin) and cellular (HSP70)] in the Amazonian warm-water fish matrinxã (Brycon amazonicus ) subjected to an acute cold shock. This species farming has been done in South America, and growth and feed conversion rates have been interesting. However, in subtropical areas of Brazil, where the water temperature can rapidly change, high rates of matrinxã mortality have been associated with abrupt decrease in the water temperature. Thus, we subjected matrinxã to a sudden cold shock by transferring the fish directly to tanks in which the water temperature was 10ºC below the initial conditions (cold shock from 28ºC to 18ºC). After 1h the fish were returned to the original tanks (28ºC). The handling associated with tank transfer was also imposed on control groups (not exposed to cold shock). While exposure to cold shock did not alter the measured physiological conditions within 1h, fish returned to the ambient condition (water at 28º C) significantly increased plasma cortisol and glucose levels. Exposure to cold shock and return to the warm water did not affect HSP70 levels. The increased plasma cortisol and glucose levels after returning the fish to warm water suggest that matrinxã requires cortisol and glucose for adaptation to increased temperature.

O presente trabalho avaliou as principais respostas fisiológicas e celulares [endócrino (cortisol), metabólico (glicose), hematológico (hematócrito and hemoglobina) e celular (HSP70)] ao estresse de um peixe de águas tépidas, o matrinxã (Brycon amazonicus ), quando submetido a um choque térmico frio abrupto. Essa espécie vem sendo amplamente cultivada na América do Sul por apresentar excelentes índices zootécnicos de crescimento e conversão alimentar. Entretanto, os produtores rurais encontram limitações no manejo do matrinxã, quando criado em regiões mais frias que sua região de origem, a Bacia Amazônica. Assim, o matrinxã foi submetido a um choque frio através da transferência direta dos peixes para tanques com água fria a 18ºC. Após 1h, esses peixes retornaram a suas caixas de origem a 28ºC. O manuseio de peixes necessário para conduzir o choque térmico experimental foi também imposto aos grupos controle, sendo, entretanto, evitada a água fria. O matrinxã demonstrou claros sinais de estresse fisiológico durante os procedimentos experimentais. Porém, essas respostas não foram associadas ao choque frio, mas sim ao choque quente por ocasião da volta dos peixes para as caixas de origem. As respostas primárias e secundárias de estresse foram evidentes através das análises plasmáticas de cortisol e glicose. Já o hematócrito, a hemoglobina e as expressões da proteína de estresse, HSP70, não foram afetadas. Nossos resultados sustentam que o matrinxã falhou em responder ao choque térmico frio, mas não ao choque térmico quente, que é um estressor evidentemente associado à origem natural dessa espécie de águas de elevadas temperaturas.

Magnetic resonance methods for studying intact spermatozoa.

Motility is used as a routine parameter for assessing spermatozoa activity. The quality rating techniques adopted are based on electron or optical microscopy. However, these methods depend on gross structural and dynamical features of sperm cells and do not provide information on metabolic activity of intact cells. Lately, biochemical assays have become popular. Such methods are cumbersome and destroy the samples. Magnetic resonance methods offer a non-invasive method for studies on intact sperms. We have investigated respiration, maturation and in vitro capacitation of sperms from human ejaculates and sperms extracted from goat reproductive organ using electron spin resonance spin labelling and [31P] nuclear magnetic resonance methods. These studies clearly establish the advantages of magnetic resonance in studies related to metabolic activity of sperms.