scholarly journals A Genome-Wide Approach to Discovery of Small RNAs Involved in Regulation of Virulence in Vibrio cholerae

2011 ◽  
Vol 7 (7) ◽  
pp. e1002126 ◽  
Author(s):  
Evan S. Bradley ◽  
Kip Bodi ◽  
Ayman M. Ismail ◽  
Andrew Camilli
Keyword(s):  
Vibrio Cholerae ◽  
Small Rnas ◽  
Genome Wide ◽  
A Genome

scholarly journals Processed Small RNAs in Archaea and BHB Elements

2015 ◽  
Vol 1 (1) ◽  
pp. 18 ◽  
Author(s):  
Sarah Juliane Berkemer ◽  
Christian Höner zu Siederdissen ◽  
Fabian Amman ◽  
Axel Wintsche ◽  
Sebastian Will ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Small Rnas ◽  
Pattern Search ◽  
Search Methods ◽  
Genome Wide ◽  
Archaeal Species ◽  
A Genome ◽  
Pattern Search Methods ◽  
Genome Wide Survey ◽  
Common Sequence

Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piece-wise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.

scholarly journals Stress Resets Transgenerational Small RNA Inheritance

2019 ◽  
Author(s):  
Leah Houri-Ze’evi ◽  
Guy Teichman ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Memory Trace ◽  
Mapk Pathway ◽  
Transgenerational Inheritance ◽  
Cultivation Conditions ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Basic Concepts

AbstractTransgenerational inheritance of small RNAs is challenging basic concepts of heredity and achieving control over such responses is of great interest. InC. elegansnematodes, small RNAs are transmitted across generations to establish a transgenerational memory trace of ancestral environments and distinguish self from non-self genes. Inheritance of small RNAs is regulated by dedicated machinery and carryover of aberrant heritable small RNA responses was shown to be maladaptive and to induce sterility. Here we show that various types of stress (starvation, high temperatures, and high osmolarity) but not non-stressful changes in cultivation conditions, lead to resetting of small RNA inheritance. We found that stress leads to a genome-wide reduction in heritable small RNA levels and that mutants defective in different stress pathways exhibit irregular RNAi inheritance dynamics. Moreover, we discovered that resetting of heritable RNAi is orchestrated by MAPK pathway factors, the transcription factor SKN-1, and the MET-2 methyltransferase. Termination of small RNA inheritance, and the fact that this process depends on stress, could protect from run-on of environment-irrelevant heritable gene regulation.

scholarly journals A small RNA pathway mediates global allelic dosage in endosperm

2017 ◽  
Author(s):  
Robert M. Erdmann ◽  
P.R. V. Satyaki ◽  
Maja Klosinska ◽  
Mary Gehring
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Inverse Relationship ◽  
Paternal Genome ◽  
Pol Iv ◽  
Genome Wide ◽  
A Genome ◽  
Normal Seed ◽  
Wide Scale ◽  
Parent Of Origin

SummaryBalance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of genes in Arabidopsis endosperm are expressed in a 2:1 maternal:paternal ratio, reflecting endosperm genomic DNA content. Here we find that the 2:1 transcriptional ratio is not, unexpectedly, a passive default but is actively regulated. We describe an inverse relationship between the parent-of-origin of small RNAs and mRNAs in endosperm on a genome-wide scale. Disruption of the Pol IV small RNA pathway causes the entire transcriptome to become more maternally biased. Furthermore, paternal inheritance of a RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. These results indicate that maintenance of the maternal:paternal transcriptome ratio in endosperm is an active process and reveal a function for RNA Pol IV in mediating the global transcriptional balance between maternally and paternally inherited genomes in endosperm.

scholarly journals Vibrio cholerae Virulence Activator ToxR Regulates Manganese Transport and Resistance to Reactive Oxygen Species

2019 ◽  
Vol 88 (3) ◽  
Author(s):  
Hang-hang Jiang ◽  
Yitian Zhou ◽  
Ming Liu ◽  
Jessie Larios-Valencia ◽  
Zachariah Lee ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Vibrio Cholerae ◽  
Reactive Oxygen ◽  
Oxygen Species ◽  
Content Type ◽  
Genome Wide ◽  
A Genome ◽  
Its Gene ◽  
Virulence Regulator ◽  
Manganese Transport

ABSTRACT Like many other pathogens, Vibrio cholerae, the causative agent of cholera, can modulate its gene expression to combat stresses encountered in both aquatic and host environments, including stress posed by reactive oxygen species (ROS). We previously reported that the virulence activator AphB in V. cholerae is involved in ROS resistance. In this study, we found that another key virulence regulator, ToxR, was important for V. cholerae resistance to hydrogen peroxide. Through a genome-wide transposon screen, we discovered that a deletion in mneA, which encodes a manganese exporter, restored ROS resistance of the toxR mutant. We then showed that ToxR did not affect mneA transcription but that the ToxR-regulated major porin OmpU was critical for ROS resistance. The addition of manganese in culture medium restored ROS resistance in both the toxR and ompU mutants. Furthermore, elemental analysis indicated that the intracellular concentration of manganese in both the toxR and ompU mutants was reduced. This may result in intracellular ROS accumulation in these mutants. Our data suggest that ToxR plays an important role in the resistance to reactive oxygen species through the regulation of manganese transport.

scholarly journals Vibrio cholerae Represses Polysaccharide Synthesis To Promote Motility in Mucosa

2015 ◽  
Vol 83 (3) ◽  
pp. 1114-1121 ◽  
Author(s):  
Zhenyu Liu ◽  
Yuning Wang ◽  
Shengyan Liu ◽  
Ying Sheng ◽  
Karl-Gustav Rueggeberg ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Epithelial Surface ◽  
Semisolid Medium ◽  
Content Type ◽  
Infant Mouse ◽  
Genome Wide ◽  
Polysaccharide Synthesis ◽  
A Genome ◽  
Rapid Spread ◽  
Colonization Model

The viscoelastic mucus layer of gastrointestinal tracts is a host defense barrier that a successful enteric pathogen, such asVibrio cholerae, must circumvent.V. cholerae, the causative agent of cholera, is able to penetrate the mucosa and colonize the epithelial surface of the small intestine. In this study, we found that mucin, the major component of mucus, promotedV. choleraemovement on semisolid medium and in liquid medium. A genome-wide screen revealed thatVibriopolysaccharide (VPS) production was inversely correlated with mucin-enhanced motility. Mucin adhesion assays indicated that VPS bound to mucin. Moreover, we found thatvpsexpression was reduced upon exposure to mucin. In an infant mouse colonization model, mutants that overexpressed VPS colonized less effectively than wild-type strains in more distal intestinal regions. These results suggest thatV. choleraeis able to sense mucosal signals and modulatevpsexpression accordingly so as to promote fast motion in mucus, thus allowing for rapid spread throughout the intestines.

scholarly journals Stress resets ancestral heritable small RNA responses

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Leah Houri Zeevi ◽  
Guy Teichman ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Memory Trace ◽  
Mapk Pathway ◽  
Transgenerational Inheritance ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Basic Concepts ◽  
Stress Dependent

Transgenerational inheritance of small RNAs challenges basic concepts of heredity. In C. elegans nematodes, small RNAs are transmitted across generations to establish a transgenerational memory trace of ancestral environments and distinguish self-genes from non-self-elements. Carryover of aberrant heritable small RNA responses was shown to be maladaptive and to lead to sterility. Here we show that various types of stress (starvation, high temperatures, and high osmolarity) induce resetting of ancestral small RNA responses and a genome-wide reduction in heritable small RNA levels. We found that mutants that are defective in various stress pathways exhibit irregular RNAi inheritance dynamics even in the absence of stress. Moreover, we discovered that resetting of ancestral RNAi responses is specifically orchestrated by factors that function in the p38 MAPK pathway and the transcription factor SKN-1/Nrf2. Stress-dependent termination of small RNA inheritance could protect from run-on of environment-irrelevant heritable gene regulation.

scholarly journals Comparative Profiling of Small RNAs Originated From Two Varieties of Chinese Cabbage (Brassica Rapa) With Distinct Leaf Traits

2021 ◽  
Author(s):  
XU XIN LIU ◽  
XIANG YU ◽  
HAN WANG ◽  
YU KE HE
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Small Rna ◽  
Small Rnas ◽  
Leaf Shape ◽  
Leaf Traits ◽  
Differentially Expressed ◽  
High Yield ◽  
Genome Wide ◽  
A Genome

Abstract The species Brassica rapa includes many important vegetable crops. For a genome-wide survey of small RNAs in B. rapa, we performed massively parallel small RNA deep sequencing by using two representative varieties of non-heading Chinese cabbage (B. rapa ssp. chinensis) that are distinct in leaf shape, size, color and curvature. In total, 13.30 million small RNA reads were generated from Huaq, a variety with up-curved blades and wide petioles, and 14.69 million for Wut, a variety with down-curved blades and narrow petioles. After normalization, about half of small RNA reads in each variety were mapped to the published reference genome of B. rapa. In Huaq seedlings, unique small RNAs were much more than in Wut seedlings. Among them, 45 miRNAs were up-regulated or down-regulated in one variety, compared with those in another variety. Numbers of ta-siRNAs (trans-acting siRNAs) and ra-siRNAs (repeat-associated siRNAs) in Huaq seedlings were more than those detected in Wut seedlings, while gene-derived siRNAs (siRNAs derived from the sense and antisense strands of annotated genes regeion) in Huaq seedlings were less than in Wut seedlings. Especially, bra-miR156, bra-miR166 and bra-miR319 and one of ta-siRNAs that play important role in leaf shape, leaf size, leaf curvature and phase transition were differentially expressed between two varieties. In addition, total number of small RNAs derived from chloroplast genome of Wut was more than that of Huaq. The differentially-expressed small RNAs on genome-wide level provides the clue for the study of small-RNA-mediated morphology of leaves and is useful for developing of small RNA markers for leaf traits desirable for high yield and quality.

Establishment of a genome-wide RNAi screen; Identification of novel genes involved in clonal maintenance of ALL

2014 ◽  
Vol 226 (03) ◽  
Author(s):  
F Ponthan ◽  
D Pal ◽  
J Vormoor ◽  
O Heidenreich
Keyword(s):  
Rnai Screen ◽  
Novel Genes ◽  
Genome Wide ◽  
A Genome
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