JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure

Troshin, Peter V; Procter, James B.; Sherstnev, Alexander; Barton, Daniel L.; Madeira, Fábio; Barton, Geoffrey J.

doi:10.1093/bioinformatics/bty045

Cited by 39 publications

(32 citation statements)

References 12 publications

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“…The amino acid sequences of conserved domains were compared and edited using Jalview software (V2.10.5) ( http://www.jalview.org/ ) 40 , and the Jalview output was submitted to JPred ( http://www.compbio.dundee.ac.uk/jabaws ) for protein secondary structure prediction using default parameters 41 .…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)

Huang

et al. 2021

Sci Rep

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Heat shock transcription factors (HSFs) are central elements in the regulatory network that controls plant heat stress response. They are involved in multiple transcriptional regulatory pathways and play important roles in heat stress signaling and responses to a variety of other stresses. We identified 41 members of the HSF gene family in moso bamboo, which were distributed non-uniformly across its 19 chromosomes. Phylogenetic analysis showed that the moso bamboo HSF genes could be divided into three major subfamilies; HSFs from the same subfamily shared relatively conserved gene structures and sequences and encoded similar amino acids. All HSF genes contained HSF signature domains. Subcellular localization prediction indicated that about 80% of the HSF proteins were located in the nucleus, consistent with the results of GO enrichment analysis. A large number of stress response–associated cis-regulatory elements were identified in the HSF upstream promoter sequences. Synteny analysis indicated that the HSFs in the moso bamboo genome had greater collinearity with those of rice and maize than with those of Arabidopsis and pepper. Numerous segmental duplicates were found in the moso bamboo HSF gene family. Transcriptome data indicated that the expression of a number of PeHsfs differed in response to exogenous gibberellin (GA) and naphthalene acetic acid (NAA). A number of HSF genes were highly expressed in the panicles and in young shoots, suggesting that they may have functions in reproductive growth and the early development of rapidly-growing shoots. This study provides fundamental information on members of the bamboo HSF gene family and lays a foundation for further study of their biological functions in the regulation of plant responses to adversity.

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Section: Methodsmentioning

confidence: 99%

Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)

Huang

et al. 2021

Sci Rep

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“… (A) Diagrams of human PUM1 and PUM2 proteins showing length in amino acid (aa) residues, sequence motifs, secondary structure, disordered versus ordered regions (computed by JRONN) [119] and hydrophobic versus hydrophilic amino acid content (adapted from Protein Data Bank: https://www.rcsb.org ). Post-translational modifications (PTM) including methylation, phosphorylation, and ubiquitylation from Uniprot ( https://www.uniprot.org ) and Phosphosite ( https://www.phosphosite.org ) are shown at the top.…”

Section: Figurementioning

confidence: 99%

Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins

2018

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Mammalian Pumilio proteins, PUM1 and PUM2, are members of the PUF family of sequence specific RNA-binding proteins. This review explores their mechanisms, regulatory networks, biological functions, and relevance to diseases. Pumilio proteins bind an extensive network of mRNAs and repress protein expression by inhibiting translation and promoting mRNA decay. Opposingly, in certain contexts they can activate protein expression. Pumilio proteins also regulate non-coding RNAs. The non-coding RNA, NORAD, can in turn modulate Pumilio activity. Genetic analysis provides new insights into Pumilio protein function. They are essential for growth and development. They control diverse processes including stem cell fate and neurological functions such as behavior and memory formation. Novel findings show that their dysfunction contributes to neurodegeneration, epilepsy, movement disorders, intellectual disability, infertility, and cancer.

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“…Based on InterProScan scanning results, AIG1 domain sequences were extracted from protein sequences of B. glabrata, and aligned using the accurate L-INS-i method [72] imbedded in the MAFFT's program [73] through the JABAWS platform [74]. AIG1 domain sequences of Pomacea canaliculata (Pc_XP_025083382.1, Pc_XP_025083383.1, and Pc_XP_025111428.1) were included in the analysis as an outgroup.…”

Section: Phylogenetic and Sequence Analysismentioning

confidence: 99%

Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni

Loker

Zhang

et al. 2020

BMC Genomics

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Background: The AIG (avrRpt2-induced gene) family of GTPases, characterized by the presence of a distinctive AIG1 domain, is mysterious in having a peculiar phylogenetic distribution, a predilection for undergoing expansion and loss, and an uncertain functional role, especially in invertebrates. AIGs are frequently represented as GIMAPs (GTPase of the immunity associated protein family), characterized by presence of the AIG1 domain along with coiled-coil domains. Here we provide an overview of the remarkably expanded AIG repertoire of the freshwater gastropod Biomphalaria glabrata, compare it with AIGs in other organisms, and detail patterns of expression in B. glabrata susceptible or resistant to infection with Schistosoma mansoni, responsible for the neglected tropical disease of intestinal schistosomiasis. Results: We define the 7 conserved motifs that comprise the AIG1 domain in B. glabrata and detail its association with at least 7 other domains, indicative of functional versatility of B. glabrata AIGs. AIG genes were usually found in tandem arrays in the B. glabrata genome, suggestive of an origin by segmental gene duplication. We found 91 genes with complete AIG1 domains, including 64 GIMAPs and 27 AIG genes without coiled-coils, more than known for any other organism except Danio (with > 100). We defined expression patterns of AIG genes in 12 different B. glabrata organs and characterized whole-body AIG responses to microbial PAMPs, and of schistosome-resistant or-susceptible strains of B. glabrata to S. mansoni exposure. Biomphalaria glabrata AIG genes clustered with expansions of AIG genes from other heterobranch gastropods yet showed unique lineage-specific subclusters. Other gastropods and bivalves had separate but also diverse expansions of AIG genes, whereas cephalopods seem to lack AIG genes. Conclusions: The AIG genes of B. glabrata exhibit expansion in both numbers and potential functions, differ markedly in expression between strains varying in susceptibility to schistosomes, and are responsive to immune challenge. These features provide strong impetus to further explore the functional role of AIG genes in the defense responses of B. glabrata, including to suppress or support the development of medically relevant S. mansoni parasites.

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JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure

Cited by 39 publications

References 12 publications

Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)

Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)

Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins

Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni

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