Modern Computational Techniques for the HMMER Sequence Analysis

Meng, Xiangru; Ji, Yanqing

doi:10.1155/2013/252183

Cited by 27 publications

(18 citation statements)

References 26 publications

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“…Then, BLASTP was used to obtain the homolog candidate sequences with E < 10 −5 . All the candidate sequences were filtered by HMMER ( Meng and Ji, 2013 ) ( E < 10 −5 ) against the Pfam database ( Finn et al, 2016 ) to ensure each sequence contained the iconic domain structures characteristic of the gene family, and the remaining sequences were considered to be the corresponding genes. All multiple-sequence alignments were performed using the MAFFT, and conservation blocks trimmed using trimAl software.…”

Section: Methodsmentioning

confidence: 99%

RETRACTED: Amino acid synthesis loss in parasitoid wasps and other hymenopterans

Xiong

Teng

et al. 2020

eLife

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Insects utilize diverse food resources which can affect the evolution of their genomic repertoire, including leading to gene losses in different nutrient pathways. Here we investigate gene loss in amino acid synthesis pathways, with special attention to hymenopterans and parasitoid wasps. Using comparative genomics, we find that synthesis capability for tryptophan, phenylalanine, tyrosine and histidine was lost in holometabolous insects prior to hymenopteran divergence, while valine, leucine and isoleucine were lost in the common ancestor of Hymenoptera. Subsequently, multiple loss events of lysine synthesis occurred independently in the Parasitoida and Aculeata. Experiments in the parasitoid Cotesia chilonis confirm that it has lost the ability to synthesize eight amino acids. Our findings provide insights into amino acid synthesis evolution, and specifically can be used to inform the design of parasitoid artificial diets for pest control.

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Section: Methodsmentioning

confidence: 99%

RETRACTED: Amino acid synthesis loss in parasitoid wasps and other hymenopterans

Xiong

Teng

et al. 2020

eLife

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“…The candidate hemomucin genes of each species were obtained by the BLASTP against the reference sequences with E-value 1E-30. Then the candidate hemomucin genes were analyzed using the HMMER [ 85 ] (version 3.1b2). To ensure reliability, the sequences short than 300 bp were removed.…”

Section: Methodsmentioning

confidence: 99%

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum

Yin

et al. 2018

BMC Genomics

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BackgroundParasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer). One striking phenomenon exhibited by M. cingulum is polyembryony, the formation of multiple genetically identical offspring from a single zygote. Moreover, M. cingulum employs a passive parasitic strategy by preventing the host’s immune system from recognizing the embryo as a foreign body. Thus, the embryos evade the host’s immune system and are not encapsulated by host hemocytes. Unfortunately, the mechanism of both polyembryony and immune evasion remains largely unknown.ResultsWe report the genome of the parasitoid wasp M. cingulum. Comparative genomics analysis of M. cingulum and other 11 insects were conducted, finding some gene families with apparent expansion or contraction which might be linked to the parasitic behaviors or polyembryony of M. cingulum. Moreover, we present the evidence that the microRNA miR-14b regulates the polyembryonic development of M. cingulum by targeting the c-Myc Promoter-binding Protein 1 (MBP-1), histone-lysine N-methyltransferase 2E (KMT2E) and segmentation protein Runt. In addition, Hemomucin, an O-glycosylated transmembrane protein, protects the endoparasitoid wasp larvae from being encapsulated by host hemocytes. Motif and domain analysis showed that only the hemomucin in two endoparasitoids, M. cingulum and Venturia canescens, possessing the ability of passive immune evasion has intact mucin domain and similar O-glycosylation patterns, indicating that the hemomucin is a key factor modulating the immune evasion.ConclusionsThe microRNA miR-14b participates in the regulation of polyembryonic development, and the O-glycosylation of the mucin domain in the hemomucin confers the passive immune evasion in this wasp. These key findings provide new insights into the polyembryony and immune evasion.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4783-x) contains supplementary material, which is available to authorized users.

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“…Because it was not clear whether EhSNXs make complex with the other major retromer subcomplex, we investigated whether EhSNXs are colocalised with Vps26 during trogocytosis of Chinese hamster ovary (CHO) cells by IFA using HA-EhSNX1-and HA-EhSNX2-expressing strains. Phox homology domain sequences were predicted by HMMER (Meng & Ji, 2013) and are shown with yellow background. To investigate the localisation and kinetics of EhSNXs during trogocytosis, we performed IFA at 15 min after addition of CellTracker Blue-stained live CHO cells to E. histolytica trophozoites.…”

Section: Immunofluorescence Imaging Showing Colocalisation Of Ehsnxmentioning

confidence: 99%

“…Protein sequences were aligned using clustalw algorithm (http:// clustalw.ddbj.nig.ac.jp). Phox homology domain sequences were predicted by HMMER (Meng & Ji, 2013) and are shown with yellow background. The numbers by three amino acid sequences (EhSNX1, EhSNX2, and HsSNX3) correspond to the a.a. positions of each protein, whereas those on top of the sequences (Arg69, Ser72, Lys95, Ile109, and Arg118) correspond to the positions of the residues in HsSNX3 (Lenoir et al, 2018).…”

Section: Immunofluorescence Imaging Showing Colocalisation Of Ehsnxmentioning

confidence: 99%

Two isotypes of phosphatidylinositol 3‐phosphate ‐ binding sorting nexins play distinct roles in trogocytosis in Entamoeba histolytica

Watanabe

Nakada‐Tsukui

Nozaki

2019

Cellular Microbiology

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Phosphatidylinositol phosphates (PIPs) function as important second messengers in many cellular events. In the human intestinal protist Entamoeba histolytica, where phagocytosis/trogocytosis plays an indispensable role in proliferation and pathophysiology during infection, various PIPs are involved in multiple steps of phago/trogocytosis. PI3-phosphate (PI3P) plays a pivotal role in the biogenesis of phagosome/trogosomes via recruitment of PI3P effectors. Because no known PI3P downstream effectors are conserved in E. histolytica, we exploited a unique method to identify the proteins PI3P dependently recruited to phagosomes. We rationalised that overexpression of PI3P-binding GFP-HrsFYVE competes for PI3P on phagosomal membranes and results in dissociation of PI3P effectors from phagosomes. EhVps26 and EhVps35, but not sorting nexins (SNXs), of the retromer complex were detected from phagosomes only without GFP-HrsFYVE overexpression. Two potential SNXs, EhSNX1 and EhSNX2, identified in the genome, possess only phox homology domain and specifically bound to PI3P, but retromer components, EhVps26 and EhVps35, did not bind to PI3P. Live and immunofluorescence imaging showed that EhSNX1 was recruited to the trogocytic cup and tunnel-like structures, and subsequently, EhSNX2 was recruited to trogosomes. Furthermore, EhSNX1, but not EhSNX2, specifically bound to Arp2/3 and EhVps26, which were localised to the tunnel-like structures and the trogosomes, respectively. EhSNX2 gene silencing increased trogocytosis, suggesting that EhSNX2 plays an inhibitory role in trogocytosis.

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Modern Computational Techniques for the HMMER Sequence Analysis

Cited by 27 publications

References 26 publications

RETRACTED: Amino acid synthesis loss in parasitoid wasps and other hymenopterans

RETRACTED: Amino acid synthesis loss in parasitoid wasps and other hymenopterans

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum

Two isotypes of phosphatidylinositol 3‐phosphate ‐ binding sorting nexins play distinct roles in trogocytosis in Entamoeba histolytica

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