scholarly journals A novel phyllosphere residentProtomycesspecies that interacts with theArabidopsisimmune system

2019 ◽  
Author(s):  
Kai Wang ◽  
Timo Sipilä ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
Pia Laine ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Loss ◽  
Signalling Pathways ◽  
Alternate Host ◽  
Single Strain ◽  
Genomic Changes ◽  
Gene Retention ◽  
Genome Wide ◽  
Host Jump

ABSTRACTWe describe the genome contents of sixProtomycesspp. that are pathogenic within the typical host range of the genus and a novelProtomycesstrain (SC29) that was previously isolated from the phylloplane of wildArabidopsis thaliana(Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinctProtomycessp. Analysis of gene family expansions, gene retention, and gene loss patterns among theseProtomycesspp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle ofProtomycesspp. was previously unknown. Genomic changes in SC29 and all otherProtomycesspp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease onArabidopsisas a single strain, but could persist in its phylloplane, while the closely relatedP. inouyeidoes not. SC29 treatedArabidopsisexhibited enhanced immunity againstBotrytis cinereainfection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novelProtomycessp. able to survive in theArabidopsisphylloplane and that phylloplane residency is an important element in the lifecycle ofProtomycesspp.

Gene loss in plants: Evidence from genome-wide phylogenetic analysis of thiamine pyrophosphate-dependent enzymes

2014 ◽  
Vol 53 (3) ◽  
pp. 221-227
Author(s):  
Xin-Min Tian ◽  
Peng Wang ◽  
Wen-Bin Hu ◽  
Da-Hai Gao ◽  
Qiong Li
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Loss ◽  
Thiamine Pyrophosphate ◽  
Genome Wide

scholarly journals Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Lingling Wang ◽  
Zhaoen Yang ◽  
Bin Zhang ◽  
Daoqian Yu ◽  
Ji Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Fiber Development ◽  
Genome Wide

scholarly journals Genome-Wide Comparative Analysis of BZR1 Transcription Factor in Zea mays

2021 ◽  
Vol 9 (5) ◽  
Author(s):  
Naureen Z ◽  
◽  
Maqsood H ◽  
Mazhar MW ◽  
Mehmood J ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Phylogenetic Analysis ◽  
Zea Mays ◽  
Transcription Factor ◽  
Stress Resistance ◽  
Restriction Analysis ◽  
Protein Sequences ◽  
Genome Wide ◽  
Restriction Sites

The BR-responsive genes are then regulated by BRASSINAZOLERESISTANT (BZR) Transcription Factors (TFs). As BRs possess numerous stress-resistant functions, BZR TFs also show activities of stress-resistance along with other developmental functions. Up to 88% similarity of protein sequences has been observed between BZR1 and BZR2 genes. Many positive roles of BZR TFs have been revealed by many studies in positively regulating the BR signal transduction in rice and maize family, but there is a very limited research is available on the BZR gene family of Zea mays. The aim of this study is to perform a wide-genome analysis of BZR1 transcription factor in Zea mays so that regulatory role of BZR TFs in BR-induced signaling pathway can be revealed. Gene structure analysis revealed the information about exons and introns. Phylogenetic analysis was done to identify the maximum likelihood among different families of BZR genes. Restriction analysis provided the information about the presence of restriction sites in Zea mays genome.

scholarly journals Genome-wide Investigation and Expression Profiles of Heat Shock Transcription Factor (HSF) Gene Family in Maize (Zea mays L.) under Different Growth Stages and Abiotic Stress Conditions

2021 ◽  
Author(s):  
Saqlain Haider ◽  
Shazia Rehman ◽  
Yumna Ahmad ◽  
Ali Raza ◽  
Javaria Tabassum ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Zea Mays ◽  
Abiotic Stress ◽  
Heat Shock ◽  
Environmental Stress ◽  
Growth Stages ◽  
Maize Genome ◽  
Class A ◽  
Genome Wide

Heat shock transcription factors (HSFs) participate in regulating many environmental stress responses and biological processes in plants. Maize (Zea mays L.) is a major cash crop that is grown worldwide. However, the growth and yield of maize are affected by several adverse environmental inputs. Therefore, investigating the factors that regulate maize growth and development and resistance to abiotic stress is an essential task for developing stress-resilient maize varieties. Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs in the maize genome. The current study identified 25 ZmHSFs, randomly distributed throughout the maize genome. Phylogenetic analysis revealed that ZmHSFs are divided into three classes and 13 sub-classes. Gene structure and protein motif analysis supported the results obtained through the phylogenetic analysis. Domain analysis showed the DNA-binding domain to be the most conserved region of ZmHSFs. Segmental duplication is shown to be responsible for the expansion of ZmHSFs. Most of the ZmHSFs are localized inside the nucleus, and the ZmHSFs which belong to the same group show similar physio-chemical properties. The 3D structures revealed comparable conserved ZmHSFs protein structures. RNA-seq analysis revealed a major role of class A HSFs including, ZmHSFA-1a and ZmHSFA-2a in all the maize growth stages, i.e., seed, vegetative, and reproductive development. Furthermore, ZmHSFs displayed an obvious spatiotemporal expression. Under abiotic stress conditions (heat, drought, cold, UV, and salinity), members of class A and B ZmHSFs are induced. Gene ontology (GO) annotation analysis indicated a major role of ZmHSFs in resistance to environmental stress and regulation of primary metabolism. Further, the protein-protein interaction analysis showed that ZmHSFs interact with several molecular chaperons and major stress-responsive proteins. To summarize, this study provides novel insights for functional studies on the ZmHSFs in maize breeding programs.

scholarly journals In silico genome-wide identification and phylogenetic analysis of the WRKY transcription factor family in sweet orange (Citrus sinensis)

2017 ◽  
Vol 11 (06) ◽  
pp. 716-726 ◽  
Author(s):  
Eduardo Goiano da Silva ◽  
◽  
Tania Mayumi Ito ◽  
Silvia Graciele Hülse de Souza ◽  
◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factor ◽  
In Silico ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Wrky Transcription Factor ◽  
Transcription Factor Family ◽  
Genome Wide

scholarly journals Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 232
Author(s):  
Weiran Zheng ◽  
Haichao Hu ◽  
Qisen Lu ◽  
Peng Jin ◽  
Linna Cai ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Chinese Wheat

Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

scholarly journals Epigenomic Analysis of RAD51 ChIP-seq Data Reveals cis-regulatory Elements Associated with Autophagy in Cancer Cell Lines

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2547
Author(s):  
Keunsoo Kang ◽  
Yoonjung Choi ◽  
Hyeonjin Moon ◽  
Chaelin You ◽  
Minjin Seo ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Homologous Recombination ◽  
Cell Lines ◽  
Regulatory Elements ◽  
Binding Motif ◽  
Genome Wide ◽  
E Box ◽  
Autophagy Pathway ◽  
Mcf 7

RAD51 is a recombinase that plays a pivotal role in homologous recombination. Although the role of RAD51 in homologous recombination has been extensively studied, it is unclear whether RAD51 can be involved in gene regulation as a co-factor. In this study, we found evidence that RAD51 may contribute to the regulation of genes involved in the autophagy pathway with E-box proteins such as USF1, USF2, and/or MITF in GM12878, HepG2, K562, and MCF-7 cell lines. The canonical USF binding motif (CACGTG) was significantly identified at RAD51-bound cis-regulatory elements in all four cell lines. In addition, genome-wide USF1, USF2, and/or MITF-binding regions significantly coincided with the RAD51-associated cis-regulatory elements in the same cell line. Interestingly, the promoters of genes associated with the autophagy pathway, such as ATG3 and ATG5, were significantly occupied by RAD51 and regulated by RAD51 in HepG2 and MCF-7 cell lines. Taken together, these results unveiled a novel role of RAD51 and provided evidence that RAD51-associated cis-regulatory elements could possibly be involved in regulating autophagy-related genes with E-box binding proteins.

scholarly journals Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Hannes Petruschke ◽  
Christian Schori ◽  
Sebastian Canzler ◽  
Sarah Riesbeck ◽  
Anja Poehlein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Intestinal Microbiota ◽  
De Novo ◽  
Bacterial Species ◽  
Intestinal Microbiome ◽  
Single Strain ◽  
Small Proteins ◽  
Human Intestinal Microbiota ◽  
Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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