Proteomics studies confirm the presence of alternative protein isoforms on a large scale

The utilization of insect-based feeds (IBF) as an alternative protein source is increasingly gaining momentum worldwide owing to recent concerns over the impact of food systems on the environment. However, its large-scale adoption will depend on farmers’ acceptance of its key qualities. This study evaluates farmer’s perceptions of commercial IBF products and assesses the factors that would influence its adoption. It employs principal component analysis (PCA) to develop perception indices that are subsequently used in multiple regression analysis of survey data collected from a sample of 310 farmers. Over 90% of the farmers were ready and willing to use IBF. The PCA identified feed performance, social acceptability of the use of insects in feed formulation, feed versatility and marketability of livestock products reared on IBF as the key attributes that would inform farmers’ purchase decisions. Awareness of IBF attributes, group membership, off-farm income, wealth status and education significantly influenced farmers’ perceptions of IBF. Interventions such as experimental demonstrations that increase farmers’ technical knowledge on the productivity of livestock fed on IBF are crucial to reducing farmers’ uncertainties towards acceptability of IBF. Public partnerships with resource-endowed farmers and farmer groups are recommended to improve knowledge sharing on IBF.

Download Full-text

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast

Genome Research ◽

10.1101/gr.243378.118 ◽

2019 ◽

Vol 29 (12) ◽

pp. 1974-1984 ◽

Cited By ~ 7

Author(s):

Wu Wei ◽

Bianca P. Hennig ◽

Jingwen Wang ◽

Yujie Zhang ◽

Ilaria Piazza ◽

...

Keyword(s):

Protein Isoforms ◽

Alternative Protein ◽

Cryptic Promoters

Download Full-text

Protein Sequencing, One Molecule at a Time

Annual Review of Biophysics ◽

10.1146/annurev-biophys-102121-103615 ◽

2022 ◽

Vol 51 (1) ◽

Author(s):

Brendan M. Floyd ◽

Edward M. Marcotte

Keyword(s):

Nucleic Acid ◽

Single Molecule ◽

Large Scale ◽

Dynamic Range ◽

Medical Diagnostics ◽

Protein Quantification ◽

Protein Sequencing ◽

Protein Isoforms ◽

Annual Review ◽

Publication Date

Despite tremendous gains over the past decade, methods for characterizing proteins have generally lagged behind those for nucleic acids, which are characterized by extremely high sensitivity, dynamic range, and throughput. However, the ability to directly characterize proteins at nucleic acid levels would address critical biological challenges such as more sensitive medical diagnostics, deeper protein quantification, large-scale measurement, and discovery of alternate protein isoforms and modifications and would open new paths to single-cell proteomics. In response to this need, there has been a push to radically improve protein sequencing technologies by taking inspiration from high-throughput nucleic acid sequencing, with a particular focus on developing practical methods for single-molecule protein sequencing (SMPS). SMPS technologies fall generally into three categories: sequencing by degradation (e.g., mass spectrometry or fluorosequencing), sequencing by transit (e.g., nanopores or quantum tunneling), and sequencing by affinity (as in DNA hybridization–based approaches). We describe these diverse approaches, which range from those that are already experimentally well-supported to the merely speculative, in this nascent field striving to reformulate proteomics. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Download Full-text

Large Scale Profiling of Protein Isoforms Using Label-Free Quantitative Proteomics Revealed the Regulation of Nonsense-Mediated Decay in Moso Bamboo (Phyllostachys edulis)

Cells ◽

10.3390/cells8070744 ◽

2019 ◽

Vol 8 (7) ◽

pp. 744 ◽

Cited By ~ 5

Author(s):

Xiaolan Yu ◽

Yongsheng Wang ◽

Markus V. Kohnen ◽

Mingxin Piao ◽

Min Tu ◽

...

Keyword(s):

Mass Spectrometry ◽

Quantitative Proteomics ◽

Large Scale ◽

Gene Annotation ◽

Function Analysis ◽

Moso Bamboo ◽

Protein Isoforms ◽

Label Free ◽

Total Proteins ◽

Protein Coding

Moso bamboo is an important forest species with a variety of ecological, economic, and cultural values. However, the gene annotation information of moso bamboo is only based on the transcriptome sequencing, lacking the evidence of proteome. The lignification and fiber in moso bamboo leads to a difficulty in the extraction of protein using conventional methods, which seriously hinders research on the proteomics of moso bamboo. The purpose of this study is to establish efficient methods for extracting the total proteins from moso bamboo for following mass spectrometry-based quantitative proteome identification. Here, we have successfully established a set of efficient methods for extracting total proteins of moso bamboo followed by mass spectrometry-based label-free quantitative proteome identification, which further improved the protein annotation of moso bamboo genes. In this study, 10,376 predicted coding genes were confirmed by quantitative proteomics, accounting for 35.8% of all annotated protein-coding genes. Proteome analysis also revealed the protein-coding potential of 1015 predicted long noncoding RNA (lncRNA), accounting for 51.03% of annotated lncRNAs. Thus, mass spectrometry-based proteomics provides a reliable method for gene annotation. Especially, quantitative proteomics revealed the translation patterns of proteins in moso bamboo. In addition, the 3284 transcript isoforms from 2663 genes identified by Pacific BioSciences (PacBio) single-molecule real-time long-read isoform sequencing (Iso-Seq) was confirmed on the protein level by mass spectrometry. Furthermore, domain analysis of mass spectrometry-identified proteins encoded in the same genomic locus revealed variations in domain composition pointing towards a functional diversification of protein isoform. Finally, we found that part transcripts targeted by nonsense-mediated mRNA decay (NMD) could also be translated into proteins. In summary, proteomic analysis in this study improves the proteomics-assisted genome annotation of moso bamboo and is valuable to the large-scale research of functional genomics in moso bamboo. In summary, this study provided a theoretical basis and technical support for directional gene function analysis at the proteomics level in moso bamboo.

Download Full-text

A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development

10.1101/2021.03.24.436683 ◽

2021 ◽

Author(s):

Andrew J Modzelewski ◽

Wanqing Shao ◽

Jingqi Chen ◽

Angus Lee ◽

Xin Qi ◽

...

Keyword(s):

Cell Proliferation ◽

Mammalian Species ◽

Embryo Implantation ◽

Preimplantation Development ◽

Protein Isoforms ◽

Specific Expression ◽

Promote Cell Proliferation ◽

Alternative Protein ◽

Evolutionarily Conserved ◽

Species Specific

Retrotransposons mediate gene regulation in multiple developmental and pathological processes. Here, we characterized the transient retrotransposon induction in preimplantation development of eight mammalian species. While species-specific in sequences, induced retrotransposons exhibit a similar preimplantation profile, conferring gene regulatory activities particularly through LTR retrotransposon promoters. We investigated a mouse-specific MT2B2 retrotransposon promoter, which generates an N-terminally truncated, preimplantation-specific Cdk2ap1ΔN isoform to promote cell proliferation. Cdk2ap1ΔN functionally contrasts to the canonical Cdk2ap1, which represses cell proliferation and peaks in mid-gestation stage. The mouse-specific MT2B2 element is developmentally essential, as its deletion abolishes Cdk2ap1ΔN, reduces cell proliferation and impairs embryo implantation. Intriguingly, Cdk2ap1ΔN is evolutionarily conserved across mammals, driven by species-specific promoters. The distinct preimplantation Cdk2ap1ΔN expression across different mammalian species correlates with their different duration in preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.

Download Full-text

Proteomics: The protein complement of the genome

The Biochemist ◽

10.1042/bio02501007 ◽

2003 ◽

Vol 25 (1) ◽

pp. 7-9

Author(s):

Hannes Ponstingl ◽

Janet M. Thornton

Keyword(s):

Messenger Rna ◽

Protein Separation ◽

Large Scale ◽

Protein Complexes ◽

Protein Isoforms ◽

Structural Proteomics ◽

Protein Markers ◽

Proteomics Data ◽

Single Experiment ◽

Large Sets

Recent advances in protein separation technology and mass spectrometry (MS) have enabled the systematic identification and quantification of large sets of proteins from an organelle, cell type or organism. In principle, protein isoforms, enzymically modified variants and protein complexes can be studied, for instance, at a certain stage in development or in response to stress or more subtle changes of the environment. An important pre-clinical application is the search for protein markers in body fluids for diagnostic purposes. Such proteomics studies can be performed increasingly at high-throughput rates that are reminiscent of those of genomic sequencing or the monitoring of messenger RNA levels. Thus, large sets of proteins can be monitored simultaneously in a single experiment. Proteomics data will increasingly be followed up by investigations of the three-dimensional structures of proteins and protein complexes at atomic detail in large-scale structural proteomics projects. We attempt in this article to give a flavour of what to us seem important experimental developments and to point to links with bioinformatics resources where appropriate.

Download Full-text

PAX8 and MECOM are interaction partners driving ovarian cancer

Nature Communications ◽

10.1038/s41467-021-22708-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Melusine Bleu ◽

Fanny Mermet-Meillon ◽

Verena Apfel ◽

Louise Barys ◽

Laura Holzer ◽

...

Keyword(s):

Ovarian Cancer ◽

Large Scale ◽

Gynecological Cancer ◽

Molecular Complexes ◽

Protein Isoforms ◽

Specific Gene ◽

Urogenital System ◽

Ovarian Cancers

AbstractThe transcription factor PAX8 is critical for the development of the thyroid and urogenital system. Comprehensive genomic screens furthermore indicate an additional oncogenic role for PAX8 in renal and ovarian cancers. While a plethora of PAX8-regulated genes in different contexts have been proposed, we still lack a mechanistic understanding of how PAX8 engages molecular complexes to drive disease-relevant oncogenic transcriptional programs. Here we show that protein isoforms originating from the MECOM locus form a complex with PAX8. These include MDS1-EVI1 (also called PRDM3) for which we map its interaction with PAX8 in vitro and in vivo. We show that PAX8 binds a large number of genomic sites and forms transcriptional hubs. At a subset of these, PAX8 together with PRDM3 regulates a specific gene expression module involved in adhesion and extracellular matrix. This gene module correlates with PAX8 and MECOM expression in large scale profiling of cell lines, patient-derived xenografts (PDXs) and clinical cases and stratifies gynecological cancer cases with worse prognosis. PRDM3 is amplified in ovarian cancers and we show that the MECOM locus and PAX8 sustain in vivo tumor growth, further supporting that the identified function of the MECOM locus underlies PAX8-driven oncogenic functions in ovarian cancer.

Download Full-text

Cell-Based Meat and Firms’ Environmental Strategies: New Rationales as per Available Literature

Sustainability ◽

10.3390/su12229418 ◽

2020 ◽

Vol 12 (22) ◽

pp. 9418

Author(s):

Germano Glufke Reis ◽

Marina Sucha Heidemann ◽

Katherine Helena Oliveira de Matos ◽

Carla Forte Maiolino Molento

Keyword(s):

Value Chain ◽

Large Scale ◽

Animal Ethics ◽

Consumer Attitudes ◽

Environmental Benefits ◽

Meat Production ◽

Review Of The Literature ◽

Production Chain ◽

Alternative Protein ◽

Environmental Strategies

Higher demand for meat production and limited inputs, as well as environmental and animal ethics issues, are bringing alternative protein sources to the market, such as cell-based meat (CBM), i.e., meat produced through cell culturing, without involving animal raising and killing. Although the potential social and environmental benefits of the technology have been recently addressed in the blossoming CBM literature, little has been discussed about the possible implications for the environmental strategies of firms that are entering the new cell-based production chain. Thus, drawing on the theoretical framework of competitive environmental strategies and a systematic review of the literature, we discuss prospects for cell-based meat regarding the possible adoption of environmental strategies by firms that are entering the CBM chain. The technology may be considered a potential means for mitigating most of the environmental impacts of large-scale meat production, e.g., extensive land use and greenhouse gas emissions. We discuss how such benefits and consumer attitudes towards cultivated meat could encourage the adoption of environmental strategies by firms, and the roles that value chain firms are likely to play in those strategies in the future.

Download Full-text