Protein diversification through post-translational modifications, alternative splicing, and gene duplication

Goldtzvik, Yonathan; Sen, Neeladri; S, Lam; Orengo, Christine A.

doi:10.1016/j.sbi.2023.102640

Cited by 13 publications

(7 citation statements)

References 88 publications

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“…Gene duplication includes whole genome duplication (polyploidization), segmental duplication, and tandem duplication, which is a very important mechanism that increases gene copy number and contributes to the generation of new genes ( Goldtzvik et al, 2023 ). Our findings showed that fragmental duplication events of SpapARFs and SpnpARFs were detected in both genomes, especially in Np-X, but no tandem duplication event occurred, suggesting that segmental duplication events are mainly promoting the expansion of the ARF gene family.…”

Section: Discussionmentioning

confidence: 99%

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Lin,

Ali,

Chu

et al. 2023

Front. Microbiol.

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Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 SpapARFs and 39 SpnpARFs were identified in two genomes of Saccharum spontaneum clones AP85-441 and Np-X, respectively. Phylogenetic analysis showed that all ARF genes were clustered into four clades, which is identical to those ARF genes in maize (Zea mays) and sorghum (Sorghum bicolor). The gene structure and domain composition of this ARF family are conserved to a large degree across plant species. The SpapARF and SpnpARF genes were unevenly distributed on chromosomes 1–8 and 1–10 in the two genomes of AP85-441 and Np-X, respectively. Segmental duplication events may also contribute to this gene family expansion in S. spontaneum. The post-transcriptional regulation of ARF genes likely involves sugarcane against various stressors through a miRNA-medicated pathway. Expression levels of six representative ShARF genes were analyzed by qRT-PCR assays on two sugarcane cultivars [LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald)] triggered by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections and salicylic acid (SA) treatment. ShARF04 functioned as a positive regulator under Xa and Aaa stress, whereas it was a negative regulator under SA treatment. ShARF07/17 genes played positive roles against both pathogenic bacteria and SA stresses. Additionally, ShARF22 was negatively modulated by Xa and Aaa stimuli in both cultivars, particularly LCP85-384. These findings imply that sugarcane ARFs exhibit functional redundancy and divergence against stressful conditions. This work lays the foundation for further research on ARF gene functions in sugarcane against diverse environmental stressors.

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Section: Discussionmentioning

confidence: 99%

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Lin,

Ali,

Chu

et al. 2023

Front. Microbiol.

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“…Gene duplication and subsequent accumulation of mutations among duplicate copies, together with sequence diversification due to speciation, represent additional mechanisms contributing to generating protein isoforms (Goldtzvik et al 2023). Duplicate copies mask the potential negative effect of new mutations and thus facilitate the accumulation of genetic diversity playing an important role in evolution.…”

Section: Isoform Diversification Of Yags Is Explained By Both Gene Du...mentioning

confidence: 99%

“…Technological advances in sequencing technologies, the invention of long-read sequencing in particular, revealed the tremendous diversity of the transcriptome (Ren et al 2023), which translates into proteome diversity (Park et al 2018;Soto et al 2019). Transcriptome diversity originates from alternative splicing and gene duplication with subsequent accumulation of mutations in duplicate copies (Goldtzvik et al 2023). In the human genome, >90% of genes undergo alternative splicing (Wang et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies

Greshnova,

Pál,

Martinez

et al. 2024

Preprint

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Y chromosomes of great apes harbor Ampliconic Genes (YAGs) - multi-copy gene families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) that encode proteins important for spermatogenesis. Previous work assembled YAG transcripts based on their targeted sequencing but not using reference genome assemblies, potentially resulting in an incomplete transcript repertoire. Here we used the recently produced gapless telomere-to-telomere (T2T) Y chromosome assemblies of great ape species (bonobo, chimpanzee, human, gorilla, Bornean orangutan, and Sumatran orangutan) and analyzed RNA data from whole-testis samples for the same species. We generated hybrid transcriptome assemblies by combining targeted long reads (Pacific Biosciences), untargeted long reads (Pacific Biosciences) and untargeted short reads (Illumina)and mapping them to the T2T reference genomes. Compared to the results from the reference-free approach, average transcript length was more than two times higher, and the total number of transcripts decreased three times, improving the quality of the assembled transcriptome. The reference-based transcriptome assemblies allowed us to differentiate transcripts originating from different Y chromosome gene copies and from their non-Y chromosome homologs. We identified two sources of transcriptome diversity - alternative splicing and gene duplication with subsequent diversification of gene copies. For each gene family, we detected transcribed pseudogenes along with protein-coding gene copies. We revealed previously unannotated gene copies of YAGs as compared to currently available NCBI annotations, as well as novel isoforms for annotated gene copies. This analysis paves the way for better understanding Y chromosome gene functions, which is important given their role in spermatogenesis.

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“…In light of this, it is reasonable to assume that the two eryngitins could be different proteolytic products derived from the same mRNA, considering the presence of a single CDS in the P. eryngii genome (see Section 2.7), in order to regulate their activity or function [23].…”

Section: Determination Of Eryngitin 3 Amino Acid Sequencementioning

confidence: 99%

The Biological Action and Structural Characterization of Eryngitin 3 and 4, Ribotoxin-like Proteins from Pleurotus eryngii Fruiting Bodies

Ragucci,

Landi,

Citores

et al. 2023

IJMS

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Ribotoxin-like proteins (RL-Ps) are specific ribonucleases found in mushrooms that are able to cleave a single phosphodiester bond located in the sarcin–ricin loop (SRL) of the large rRNA. The cleaved SRL interacts differently with some ribosomal proteins (P-stalk). This action blocks protein synthesis because the damaged ribosomes are unable to interact with elongation factors. Here, the amino acid sequences of eryngitin 3 and 4, RL-Ps isolated from Pleurotus eryngii fruiting bodies, were determined to (i) obtain structural information on this specific ribonuclease family from edible mushrooms and (ii) explore the structural determinants which justify their different biological and antipathogenic activities. Indeed, eryngitin 3 exhibited higher toxicity with respect to eryngitin 4 against tumoral cell lines and model fungi. Structurally, eryngitin 3 and 4 consist of 132 amino acids, most of them identical and exhibiting a single free cysteinyl residue. The amino acidic differences between the two toxins are (i) an additional phenylalanyl residue at the N-terminus of eryngitin 3, not retrieved in eryngitin 4, and (ii) an additional arginyl residue at the C-terminus of eryngitin 4, not retrieved in eryngitin 3. The 3D models of eryngitins show slight differences at the N- and C-terminal regions. In particular, the positive electrostatic surface at the C-terminal of eryngitin 4 is due to the additional arginyl residue not retrieved in eryngitin 3. This additional positive charge could interfere with the binding to the SRL (substrate) or with some ribosomal proteins (P-stalk structure) during substrate recognition.

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Protein diversification through post-translational modifications, alternative splicing, and gene duplication

Cited by 13 publications

References 88 publications

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies

The Biological Action and Structural Characterization of Eryngitin 3 and 4, Ribotoxin-like Proteins from Pleurotus eryngii Fruiting Bodies

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