The Sperm Proteome of the Echiuran <i>Urechis unicinctus</i> (Annelida, Echiura)

Qin, Zhenkui; Zhang, Yanjie; Mu, Huawei; Zhang, Zhifeng; Qiu, Jian‐Wen

doi:10.1002/pmic.201800107

Cited by 6 publications

(5 citation statements)

References 24 publications

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“…Urechis unicinctus, commonly known as the sea intestine, attaches to Echiuroidea and is a bentonic organism that commonly inhabits the intertidal zone and sublittoral zone along the coasts of the Huanghai Sea and the Bohai Sea. It possesses high culinary and medical value .…”

Section: Introductionmentioning

confidence: 99%

Analysis of Raman Spectra by Using Deep Learning Methods in the Identification of Marine Pathogens

et al. 2021

Anal. Chem.

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The need for efficient and accurate identification of pathogens in seafood and the environment has become increasingly urgent, given the current global pandemic. Traditional methods are not only time consuming but also lead to sample wastage. Here, we have proposed two new methods that involve Raman spectroscopy combined with a long short-term memory (LSTM) neural network and compared them with a method using a normal convolutional neural network (CNN). We used eight strains isolated from the marine organism Urechis unicinctus, including four kinds of pathogens. After the models were configured and trained, the LSTM methods that we proposed achieved average isolation-level accuracies exceeding 94%, not only meeting the requirement for identification but also indicating that the proposed methods were faster and more accurate than the normal CNN models. Finally, through a computational approach, we designed a loss function to explore the mechanism reflected by the Raman data, finding the Raman segments that most likely exhibited the characteristics of nucleic acids. These novel experimental results provide insights for developing additional deep learning methods to accurately analyze complex Raman data.

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Section: Introductionmentioning

confidence: 99%

Analysis of Raman Spectra by Using Deep Learning Methods in the Identification of Marine Pathogens

et al. 2021

Anal. Chem.

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“…Nevertheless, little is known about sperm proteins that are involved in other critical steps of the fertilization process, such as sperm locomotion and penetration into the egg. Proteomics has been shown to be a promising tool to rapidly profile sperm proteome, but its application in free-spawning invertebrates has been limited to only few species: the Biwa pearly mussel Hyriopsis schlegelii, [10] the red abalone Haliotis rufescens, [11] the blue mussel M. edulis, [12] the Mediterranean mussel Mytilus galloprovincialis, [13] the echiuran Urechis unicinctus, [14] and the Pacific oyster C. gigas. [15,16] The two previous studies of oyster sperm proteome have both used C. gigas as the study animal, and applied 2D gel electrophoresis-based techniques.…”

Section: Doi: 101002/pmic202000167mentioning

confidence: 99%

“…Raw mass spectrometry data were converted into .mgf files using Proteome Discovery 1.3.0.339 (Thermo Finnigan) and submitted to Mascot version 2.3.2 (Matrix Sciences) to search against a C. hongkongensis genomic database with 71 248 amino acid sequences including both targets and decoys. The searching parameters were identical to those described in Qin et al (2018): [14] fixed modification for carbamidomethyl of cysteine, variable modification for oxidation of methionine, and deamidation of glutamine and asparagine; one maximum missed cleavage of trypsin; 5 ppm for peptide mass tolerance and 20 mmu for MS/MS tolerance. Proteins which met the following criteria were retained as valid identification: matched peptides with an ion score ≥ 20 (corresponding to 95% confidence level); peptide length > 7 amino acids; FDR < 0.01 at the protein level; proteins detected in all of the three biological replicates.…”

Section: Doi: 101002/pmic202000167mentioning

confidence: 99%

“…This result is similar to the sperm proteome results of the mussel M. galloprovincialis [ 13 ] and the echiuran U. unicinctus . [ 14 ] The “energy metabolism” group was further classified into more detailed functional groups: energy homeostasis (31%), tricarboxylic acid cycle (19%), electron transport chain (18%), fatty acid metabolism (16%), and glycolysis and gluconeogenesis (16%). This result was consistent with the GO classification that “catalytic activity” was the most abundant GO molecular function term ( Figure S1, Supporting Information ).…”

Section: Figurementioning

confidence: 99%

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The Sperm Proteome of the Oyster Crassostrea hongkongensis

Zhang

et al. 2020

Proteomics

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Sperm proteins play vital roles in fertilization, but little is known about their identities in free-spawning marine invertebrates. Here, 286 sperm proteins are reported from the Hong Kong oyster Crassostrea hongkongensis using label-free and semi-quantitative proteomics. Proteins extracted from three sperm samples are separated by SDS-PAGE, analyzed by LC-MS/MS, and identified using Mascot. Functional classification of the sperm proteome reveals energy metabolism (33%), signaling and binding (23%), and protein synthesis and degradation (12%) as the top functional categories. Comparison of orthologous sperm proteins between C. hongkongensis, Crassostrea gigas, Mytilus edulis, and M. galloprovincialis suggests that energy metabolism (48%) is the most conserved functional group. Sequence alignment of the C. hongkongensis bindin, an acrosomal protein that binds the sperm and the egg, with those of three other Crassostrea species, reveals several conserved motifs. The study has enriched the data of invertebrate sperm proteins and may contribute to studies of mechanisms of fertilization in free-spawning invertebrates. The proteomic data are available in ProteomeXchange with the identifier PXD018255. Many groups of invertebrates adopt free-spawning as the reproductive strategy, releasing large numbers of sperm and eggs into the water column where they meet and fertilize. These

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“…U. unicinctus possesses high economic value because of great edible value and potential medical value [ 23 ]. U. unicinctus is also mostly used to study gametogenesis [ 24 ], development [ 25 – 31 ], evolution [ 32 , 33 ], and sulfide metabolism [ 34 ] because of its characteristics such as a large number of eggs laid, high fertilization rate, biphasic life cycle, and high sulfide tolerance ability. Recently, the use of U. unicinctus in evo-devo studies has generated many breakthrough [ 32 , 33 ].…”

Section: Introductionmentioning

confidence: 99%

Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data

Chen,

Wang,

Yang

et al. 2023

BMC Genomics

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Background Real-time quantitative PCR (RT-qPCR) is a crucial and widely used method for gene expression analysis. Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. Commonly used reference genes are not always stable in various organisms or under different environmental conditions. With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes. Results In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus, resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. Subsequently, ten genes including five new candidate reference genes and five commonly used reference genes, were validated by RT-qPCR. The expression stability of the ten genes was analyzed using four methods (geNorm, NormFinder, BestKeeper, and ∆Ct). The comprehensive results indicated that the new candidate reference genes were more stable than most commonly used reference genes. The commonly used ACTB was the most unstable gene. The candidate reference genes STX12, EHMT1, and LYAG were the most stable genes in early development, normal adult tissues, and hindgut under sulfide stress, respectively. The log2(TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = − 0.5405 log2(TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data. Conclusion Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus.

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The Sperm Proteome of the Echiuran Urechis unicinctus (Annelida, Echiura)

Cited by 6 publications

References 24 publications

Analysis of Raman Spectra by Using Deep Learning Methods in the Identification of Marine Pathogens

Analysis of Raman Spectra by Using Deep Learning Methods in the Identification of Marine Pathogens

The Sperm Proteome of the Oyster Crassostrea hongkongensis

Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data

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