Comparative Genetics of the rdar Morphotype in Salmonella

ABSTRACT The Salmonella rdar morphotype is a distinct, rough and dry colony morphology formed by the extracellular interaction of thin aggregative fimbriae (Tafi or curli), cellulose, and other polysaccharides. Cells in rdar colonies are more resistant to desiccation and exogenous stresses, which is hypothesized to aid in the passage of pathogenic Salmonella spp. between hosts. Here we analyzed the genetic and phenotypic conservation of the rdar morphotype throughout the entire Salmonella genus. The rdar morphotype was conserved in 90% of 80 isolates representing all 7 Salmonella groups; however, the frequency was only 31% in a reference set of 16 strains (Salmonella reference collection C [SARC]). Comparative gene expression analysis was used to separate cis- and trans-acting effects on promoter activity for the 16 SARC strains, focusing on the 780-bp intergenic region containing divergent promoters for the master regulator of the rdar morphotype (agfD) and the Tafi structural genes (agfB). Surprisingly, promoter functionality was conserved in most isolates, and loss of the phenotype was due primarily to defects in trans-acting regulatory factors. We hypothesize that trans differences have been caused by domestication, whereas cis differences, detected for Salmonella enterica subsp. arizonae isolates, may reflect an evolutionary change in lifestyle. Our results demonstrate that the rdar morphotype is conserved throughout the salmonellae, but they also emphasize that regulation is an important source of variability among isolates.

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Metabolic Profiling and Gene Expression Analysis Unveil Differences in Flavonoid and Lipid Metabolisms Between ‘Huapi’ Kumquat (Fortunella crassifolia Swingle) and Its Wild Type

Frontiers in Plant Science ◽

10.3389/fpls.2021.759968 ◽

2021 ◽

Vol 12 ◽

Author(s):

Qiaoli Ma ◽

Yongwei Hu ◽

Xinghua Dong ◽

Gaofeng Zhou ◽

Xiao Liu ◽

...

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Metabolic Profiling ◽

Gene Expression Analysis ◽

Structural Genes ◽

Wild Type ◽

Gene Expressions ◽

Oil Glands ◽

Light Color ◽

Metabolomics Analysis

To elucidate the mechanism underlying special characteristic differences between a spontaneous seedling mutant ‘Huapi’ kumquat (HP) and its wild-type ‘Rongan’ kumquat (RA), the fruit quality, metabolic profiles, and gene expressions of the peel and flesh were comprehensively analyzed. Compared with RA, HP fruit has distinctive phenotypes such as glossy peel, light color, and few amounts of oil glands. Interestingly, HP also accumulated higher flavonoid (approximately 4.1-fold changes) than RA. Based on metabolomics analysis, we identified 201 differential compounds, including 65 flavonoids and 37 lipids. Most of the differential flavonoids were glycosylated by hexoside and accumulated higher contents in the peel but lower in the flesh of HP than those of RA fruit. For differential lipids, most of them belonged to lysophosphatidycholines (LysoPCs) and lysophosphatidylethanolamines (LysoPEs) and exhibited low abundance in both peel and flesh of HP fruit. In addition, structural genes associated with the flavonoid and lipid pathways were differentially regulated between the two kumquat varieties. Gene expression analysis also revealed the significant roles of UDP-glycosyltransferase (UGT) and phospholipase genes in flavonoid and glycerophospholipid metabolisms, respectively. These findings provide valuable information for interpreting the mutation mechanism of HP kumquat.

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MHC II+ resident peritoneal and pleural macrophages rely on IRF4 for development from circulating monocytes

Journal of Experimental Medicine ◽

10.1084/jem.20160486 ◽

2016 ◽

Vol 213 (10) ◽

pp. 1951-1959 ◽

Cited By ~ 51

Author(s):

Ki-Wook Kim ◽

Jesse W. Williams ◽

Ya-Ting Wang ◽

Stoyan Ivanov ◽

Susan Gilfillan ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Surface Markers ◽

Oral Antibiotics ◽

Blood Monocytes ◽

Regulatory Factors ◽

Common Features ◽

Mhc Ii

Peritoneal and pleural resident macrophages in the mouse share common features and in each compartment exist as two distinct subpopulations: F4/80+ macrophages and MHC II+ CD11c+ macrophages. F4/80+ macrophages derive from embryonic precursors, and their maintenance is controlled by Gata6. However, the origin and regulatory factors that maintain MHC II+ macrophages remain unknown. Here, we show that the MHC II+ macrophages arise postnatally from CCR2-dependent precursors that resemble monocytes. Monocytes continuously replenish this subset through adulthood. Gene expression analysis identified distinct surface markers like CD226 and revealed that the transcription factor IRF4 was selectively expressed in these macrophages relative to other organs. Monocytes first entered peritoneal or pleural cavities to become MHC II+ cells that up-regulated CD226 and CD11c later as they continued to mature. In the absence of IRF4 or after administration of oral antibiotics, MHC II+CD226−CD11c− monocyte-derived cells accumulated in peritoneal and pleural cavities, but CD11c+ CD226+ macrophages were lost. Thus, MHC II+ resident peritoneal and pleural macrophages are continuously replenished by blood monocytes recruited to the peritoneal and pleural cavities constitutively, starting after birth, where they require IRF4 and signals likely derived from the microbiome to fully differentiate.

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