Antibacterial characterization of Bacillus velezensis LG37 and mining of genes related to biosynthesis of antibacterial substances

Bacillus velezensis LG37 secretes various antibacterial substances and inhibits the growth of other bacteria. Here, we analyzed the antibacterial characteristics and the screening and verification of genes related to the synthesis of the antibacterial substance of LG37 by antibacterial activities experiment, Local BLAST+, and RT-PCR. LG37 was isolated from aquaculture water and preserved in our laboratory. The phylogenetic tree was used to analyze the genetic relationship between LG37 and the bacteriostatic test indicator strain. LG37 had a more substantial inhibitory effect on closely related strains, while the inhibitory effect on the more distantly related strains was weak. Combined with the results of genome sequencing, the ribosomal peptide (RP) bacteriocin gene and non-ribosomal peptide synthetase (NRPSs) related gene clusters were screened and analyzed. A total of six gene-coding RP bacteriocins and two genes coding surfactins and fengycin A NRPSs gene cluster were screened. Local BLAST+ analysis revealed a total of 11 NRPSs gene clusters. The active expression of the NRPSs and RP encoding genes was further validated by RT-PCR. The findings revealed various genes and gene clusters encoding RP bacteriocins and NRPSs in B. velezensis LG37. The bacterium is potentially valuable in diverse applications in aquaculture

Expression of HIV-1 genes in podocytes alone can lead to the full spectrum of HIV-1-associated nephropathy

Expression of HIV-1 genes in podocytes alone can lead to the full spectrum of HIV-1-associated nephropathy.BackgroundHuman immunodeficiency virus (HIV)-1-associated nephropathy (HIVAN) is characterized by collapsing focal and segmental glomerulosclerosis (FSGS) and microcystic tubular dilatation. HIV-1 infection is also associated with other forms of nephropathy, including mesangial hyperplasia. Since HIV-1 gene products are detected in podocytes and other renal cells, it remains uncertain whether podocyte-restricted HIV-1 gene expression can account for the full spectrum of renal lesions involving nonpodocytes.MethodsTo define the role of podocyte-restricted HIV-1 gene expression in the progression of HIVAN, we generated transgenic mice that express nonstructural HIV-1 genes selectively in podocytes.ResultsFour of the seven founder mice developed proteinuria and nephropathy. In a subsequently established transgenic line, reverse transcription-polymerase chain reaction (RT-PCR) analysis detected mRNAs for vif, vpr, nef, and spliced forms of tat and rev, but not vpu, in the kidney. In situ hybridization localized HIV-1 RNA to the podocyte. Transgenic mice on FVB/N genetic background exhibited cuboidal morphology of podocytes with reduced extension of primary and foot processes at 2 weeks of age. After 3 weeks of age, these mice developed massive and nonselective proteinuria with damage of podocytes and other glomerular cells and, after 4 weeks of age, collapsing FSGS and microcystic tubular dilatation. In marked contrast, transgenic mice with C57BL/6 genetic background showed either normal renal histology or only mild mesangial expansion without overt podocyte damage.ConclusionThe present study demonstrates that podocyte-restricted expression of HIV-1 gene products is sufficient for the development of collapsing glomerulosclerosis in the setting of susceptible genetic background

Hormone-dependent control of developmental timing through regulation of chromatin accessibility

Specification of tissue identity during development requires precise coordination of gene expression in both space and time. Spatially, master regulatory transcription factors are required to control tissue-specific gene expression programs. However, the mechanisms controlling how tissue-specific gene expression changes over time are less well understood. Here, we show that hormone-induced transcription factors control temporal gene expression by regulating the accessibility of DNA regulatory elements. Using the Drosophila wing, we demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. We also uncover a temporal cascade of transcription factors following a pulse of the steroid hormone ecdysone such that different times in wing development can be defined by distinct combinations of hormone-induced transcription factors. Finally, we show that the ecdysone-induced transcription factor E93 controls temporal identity by directly regulating chromatin accessibility across the genome. Notably, we found that E93 controls enhancer activity through three different modalities, including promoting accessibility of late-acting enhancers and decreasing accessibility of early-acting enhancers. Together, this work supports a model in which an extrinsic signal triggers an intrinsic transcription factor cascade that drives development forward in time through regulation of chromatin accessibility

A Rice Plastidial Nucleotide Sugar Epimerase Is Involved in Galactolipid Biosynthesis and Improves Photosynthetic Efficiency

Photosynthesis is the final determinator for crop yield. To gain insight into genes controlling photosynthetic capacity, we selected from our large T-DNA mutant population a rice stunted growth mutant with decreased carbon assimilate and yield production named photoassimilate defective1 (phd1). Molecular and biochemical analyses revealed that PHD1 encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. The chloroplast localization of PHD1 was confirmed by immunoblots, immunocytochemistry, and UGE activity in isolated chloroplasts, which was approximately 50% lower in the phd1-1 mutant than in the wild type. In addition, the amounts of UDP-glucose and UDP-galactose substrates in chloroplasts were significantly higher and lower, respectively, indicating that PHD1 was responsible for a major part of UGE activity in plastids. The relative amount of monogalactosyldiacylglycerol (MGDG), a major chloroplast membrane galactolipid, was decreased in the mutant, while the digalactosyldiacylglycerol (DGDG) amount was not significantly altered, suggesting that PHD1 participates mainly in UDP-galactose supply for MGDG biosynthesis in chloroplasts. The phd1 mutant showed decreased chlorophyll content, photosynthetic activity, and altered chloroplast ultrastructure, suggesting that a correct amount of galactoglycerolipids and the ratio of glycolipids versus phospholipids are necessary for proper chloroplast function. Downregulated expression of starch biosynthesis genes and upregulated expression of sucrose cleavage genes might be a result of reduced photosynthetic activity and account for the decreased starch and sucrose levels seen in phd1 leaves. PHD1 overexpression increased photosynthetic efficiency, biomass, and grain production, suggesting that PHD1 plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity. These findings will be useful for improving crop yields and for bioenergy crop engineering

Chromatin Structure Changes During Terminal Differentiation and Cell Cycle Exit in Drosophila melanogaster

During development, the number of cell divisions must be precisely controlled in order to produce tissues of the correct shape, composition and size. The majority of cells complete their final cell cycle during a process called terminal differentiation, where cells acquire cell type specific characteristics. Most terminally differentiated cells will remain in a post-mitotic or G0 state permanently to carry out critical physiological functions in tissues and organs. The enforcement of cell cycle exit is thought to be critical for proper differentiation, but how these events are coordinated in most tissues remains unclear. Chromatin accessibility and organization plays a critical role in regulating gene expression during differentiation and changes in chromatin organization also occur upon entry into G0. In my thesis research I addressed how chromatin organization and accessibility changes during terminal differentiation and cell cycle exit in the Drosophila melanogaster (fruit fly) wing. To examine the relationship between cell cycle exit and chromatin structure during terminal differentiation, I characterized the temporal changes in chromatin accessibility and gene expression during the process of terminal differentiation in the wing. This revealed changes in chromatin accessibility and gene expression that are coordinated with the transition from a proliferating to postmitotic state. To identify which changes are a consequence of cell cycle exit, I genetically disrupted cell cycle exit and examined the effects on chromatin accessibility and gene expression. This uncovered mutual cross-talk between a subset of genes in the wing terminal differentiation program and the cell cycle machinery. However, most chromatin changes including those at cell cycle genes, appear to be developmentally controlled in a manner independent of cell cycling status. Higher order chromatin organization such as the clustering of heterochromatin in the nucleus is also impacted by cell cycle exit and terminal differentiation. I found that heterochromatin clusters as cells exit the cell cycle and terminally differentiate. Heterochromatin associated modifications have been implicated in the silencing of cell cycle genes and facilitating G0. I rigorously tested this model and found that compromising heterochromatin-dependent gene silencing does not disrupt cell cycle exit. Instead, delaying or preventing cell cycle exit disrupts heterochromatin clustering and globally alters chromatin modifications, revealing that heterochromatin clustering during terminal differentiation is a consequence of cell cycle exit, rather than differentiation.PHDMolecular, Cellular, and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/143916/1/myiqin_1.pd