In silico identification and functional annotation of universal stress protein (USP) gene family in Chenopodium quinoa

Identification, sequence retrieval of USPs and their domain analysis

By using the ATUSP sequences and using BLASTP, 41 CqUSP genes have been identified in this study. The CDS sequence length ranges from 354 to 3235 bp. These putative genes’ amino acid sequence length ranges from 117 to 758. The longer the protein sequence, the more domains there are than the shorter ones. A protein’s isoelectric point (pI) is the pH at which its net charge is zero. As a result, proteins are positively charged at pH levels lower than their pI and negatively charged at pH levels higher. The protein pI ranges from strongly acidic to highly alkaline, with values ranging from 4.0 to 12.0. The isoelectric points of the putative CqUSP proteins ranged from 4.72–9.86, which shows they might exist in acidic to basic environments. The aliphatic index ranged from 33.6–109.8. The predicted half-life of these proteins in different environments is as follows: (i). In in-vitro mammalian cell culture, it is ~ 30 h, (ii). In in-vivo yeast cells, it’s > 20 h, and lastly, (iii). In E. coli, it is > 10 h. GRAVY score ranged from − 0.7–0.32. Most proteins are hydrophilic as their location is also within organelles and cells. The instability index tells whether these proteins will be stable in a test tube. It was ranged from 21.99 to 83.38 out of 42, 23 gene products showed to be stable with these values. The complete physiochemical properties of the identified genes are provided in Supplementary Table S1.

While confirming the domains of the USP proteins in quinoa, we found that out of 41 CqUSP proteins, 31 of them contain a single USP domain (Pfam00582), while the other 9 have Pkinase (Pfam00069). One of them includes the Pyr_redox (pfam00070) domain, also known as the pyridine nucleotide-disulfide oxidoreductase domain, which is a conserved protein domain involved in redox reactions. It is also present in these proteins along with USP, which helps us understand its role during oxidative stress response mechanisms. The protein kinase domain transfers phosphate groups to target proteins, regulating their activity and function. It plays a key role in cell signalling, growth, and response to stimuli such as abiotic and biotic stresses. The pyr-redox domain is a conserved protein domain involved in redox reactions. Proteins containing this domain function as oxidoreductases, catalysing the transfer of electrons from a donor molecule to an acceptor molecule. They play critical roles in metabolism, energy production, and redox signalling Fig. 2.

Multiple sequence alignment and phylogenetic analysis

Multiple sequence alignment revealed conserved regions, highlighting functionally and structurally important areas, and provided insights into the sequences’ evolutionary relationships. The protein sequences from A. thaliana and C. quinoa were aligned, and conserved regions were observed. The results of the phylogenetic analysis showed two separate branches in the tree Fig. 3. Categorisation was done on the basis of domain architecture.USP genes either have a single USP domain or a USP domain with an extra kinase domain from one of the main families of protein kinases and another domain, pyr-redoxin. An overabundance of low-frequency alleles, implying a population expansion, purifying selection, or selective sweep, was suggested by Tajima’s neutrality test value of − 0.439898125, less than zero.

Phylogenetic tree of Arabidopsis thaliana and Chenopodium quinoa. The tree is divided into two clades. The green color indicates sequences with only the USP domain, whereas the yellow color indicates all those sequences that contain other domains as well.

Structural and functional analysis of CqUSP Genes: Gene architecture, motif patterns, and amino acid composition

The gene structure was analysed to check the intronic and exonic distribution and to understand protein production from a combination of different transcripts. Upon analysis, there were 1–9 introns and 2–10 exons in the gene structure. Various introns and exons give insights into its differential fusion Fig. 4. Motifs give characteristic functioning to the proteins. In the identified sequences, motifs two and 8 are present ubiquitously and are characteristic of the USPA domain. Proteins with only the USP domain have motifs 1, 3, and 5 are also present along with 2 and 8. Motif 9 is present in the sequences with the pyr-redox domain and sequences with the kinase domain, as shown in Fig. 5. The description and properties of motif logos are provided in Supplementary Table S2. The CqUSP proteins exhibited comparable patterns of various amino acids in their composition.

Identified gene structure of CqUSPs.

Identified motif pattern of the CqUSPs.

Furthermore, the composition of amino acids was analysed as well, with different proportions revealing that CqUSPs with similar domain patterns show comparable amino acid content. In contrast, CqUSPs with distinct domain patterns show a minor variation in the amino acid composition. The amino acid makeup of AUR62016751, AUR62033121, AUR62007707, and AUR62039147 may be examined to see if they have distinct domain patterns. Specifically, AUR62016751 includes only one USP domain, whereas AUR62033121 is an extra USP domain. In addition to the USP domain, AUR62007707 contains protein kinase, whereas AUR62039147 contains a pyr_redox domain. Therefore, they possess distinct compositions as well. Supplementary Table S3 and Supplementary Fig. S1. Gene structure, motif, and amino acid data show consistent domain architecture.

Chromosomal mapping and gene duplication

C. quinoa is an allotetraploid species, which means it has two sets of chromosomes from different ancestral species. The identified sequences were on different scaffolds, mapped with reference chromosomal genome assembly of C. quinoa. There are 18 chromosomes, and localisation of the 41 CqUSP genes revealed that they are unevenly present on all chromosomes except chromosome numbers 2 and 13 Fig. 6. Chromosome 16 contains the most genes, i.e., 6, followed by chromosomes 18 and 13 with 5 and 4 genes, respectively. The number of genes existing on various separate chromosomes indicates that these genes occurred at diverse chromosomal sites because of duplication events. The duplication study showed that 15 gene pairs underwent a single tandem duplication, while the remaining 14 gene pairs were classified as segmental duplications. The divergence period was estimated to be around 0.01 million years ago (MYA) and was determined using the Ka to Ks ratio. Additionally, the analysis revealed that the selection pressure was deemed positive due to the ka/ks ratio being less than 1.

Chromosomal location of the CqUSPs.

Subcellular localisation and functional annotation of the CqUSP genes

The examination of the identified proteins’ subcellular localisation reveals that these genes demonstrate expression throughout many cellular compartments and engage in various functions. The findings showed the existence of these proteins in the cytoplasm endoplasmic reticulum, mitochondria, cytoskeleton, chloroplast, and nucleus. Additionally, they may be found inside the extracellular matrix, with a few also situated in peroxisomes, indicating their role in anoxic conditions and peroxidase activities. The heat map’s intensity indicates the pronounced localisation of these genes inside the nucleus, cytoplasm, and chloroplast. The majority of these proteins are located in the nucleus, chloroplast, and cytoplasm. Their location forecasts their involvement in several biological, molecular, and cellular processes. Their nuclear localisation pattern indicates a potential function in the transcriptional regulation of other genes and signalling networks Fig. 7.

Subcellular localization of the CqUSPs.

Functional annotation of genes was checked and revealed that these genes perform in all cellular, molecular, or biological processes. Genes were screened for biological processes and following GO IDS were matched: GO:0016310, GO:0006468 phosphorylation and protein phosphorylation, GO:0036211, GO:0006464 involved in modifications of cellular proteins, GO:0006793 and GO:0006796 phosphorus metabolisms, GO:0043412 macromolecule modification GO:0044267, GO:0019538 metabolic processes for proteins, GO:1901564 involved in metabolism of the organonitrogen compound, GO:0009409 and GO:0009266 response to heat and cold stimulus, GO:0009628 for response to abiotic stresses. These results indicate that most of the proteins with the kinase domain are involved in the phosphorylation processes. In contrast, the ones with a single USP domain are mostly involved in the metabolic process and modifications of the protein groups. These results also show they might be involved in the process corresponding to abiotic stresses such as temperature. The genes were also screened for molecular functions and the matched GO terms were GO:0004672 protein kinase activity, GO:0005524 ATP binding, GO:0016301 kinase activity, GO:0016772 transferase activity transferring phosphorus-containing groups, GO:0016773 phosphotransferase activity alcohol group as acceptor, GO:0017076 purine nucleotide binding, GO:0030554 adenyl nucleotide binding, GO:0032553 ribonucleotide binding, GO:0032555 purine ribonucleotide binding, GO:0032559 adenyl ribonucleotide binding, GO:0035639 purine ribonucleoside triphosphate binding, GO:0097367 carbohydrate derivative binding, GO:0140096 catalytic activity acting on a protein. The results of the cellular compartment validated that these genes were localised in the cytoplasm, chloroplast, and nucleus, as many of the terms associated were with intracellular entities and organelles. The mapped Go terms for these were: GO:0005886 Plasma membrane, GO:0016020 membrane, GO:0071944 cell periphery, GO:0110165, cellular anatomical entity, GO:0005622 intracellular anatomical structure, GO:0005634 nucleus, GO:0005737 Cytoplasm, GO:0035859 Seh1-associated complex, GO:0043226 organelle, GO:0043227 membrane-bounded organelles, and GO:0009536 plastid Supplementary Table S4.

Mapping cis-regulatory elements in C. quinoa USP gene promoters

The Promoter regions extracted from databases were utilised to categorise cis-regulatory elements (CREs) that may regulate gene activation under specific conditions. The analysis revealed the prevalence of 100 regulatory sequence logos located in the upstream regions of the genes. The motifs are categorised into seven distinct classes of CREs: 8% of the elements are classified as light-response elements (LREs), 7% as hormone-response elements (HREs), 3% are associated with development, 60% are identified as promoter elements, 12% pertain to abiotic stress, 3% are responsive to biotic stress, and the remaining 7% consist of elements with unknown functions Supplementary Fig. 2.

Seven promoter-related elements have been identified in these genes. These include AT-rich element, A-box, AT ~ TATA-box, TATA-box, CAAT-box, and unnamed-1. Among the most prevalent cis-regulatory elements situated upstream of the start codon are the CAAT-box and TATA-box, found at the -10 and -35 positions, respectively. TATA-box is the most abundant regulatory motif present in the upstream regions of these genes. Being a core promoter means they are present ubiquitously to initiate transcription as they are binding sites for the transcription machinery Supplementary Fig. 3.

Light responsive elements (LRE) identified were G-box, TCT-motif, AE-box, GATA-motif, Sp1, GT1-motif, Box 4, ACE, LAMP-element, GA-motif, Gap-box, ATCT-motif, 3-AF1binding Site, chs-CMA1a, chs-CMA2a, chs-Unit 1 m 1, AT1-motif, ATC-motif, TCCC-motif, Box II, Box III, I-box, L-box, 3-AF3 binding Site, ACA-Motif, AAAC-motif. These are intended to stimulate distinct photosystems and elicit a light-induced reaction. The elements that were present in large quantities were G-Box, Box 4, and GT1-motif. The data also revealed the proximity of two or more elements from these classes, suggesting that activating these promoters necessitates several components. One genetic factor for the regulation of circadian rhythms is the G-box. Furthermore, it could be involved in light signalling pathways and is the most common light-responsive element reported from DNA sequences. Based on the identification of LREs in these regions indicates that genes may have a pivotal role in the activating of light-governed reactions as well as in the modulation of transcription for chlorophyll production Supplementary Fig. 4.

The promoter regions of the CqUSPs contain the regulatory components associated with the hormones. There have been components found, which may have been classified into six main types. Class 1 includes elements related to abscisic acid termed ABA), specifically ABRE3a, AT ~ ABRE, ABRE, and ABRE4. 2nd class encompasses components associated with auxins, including TGA-element, AuxRE-Core, AuxRE, and TGA-box. Furthermore, the TGACG motif, JERE and CGTCA motif are linked to jasmonic acid are also present. The fourth class pertains to salicylic acid (SA). It encompasses salicylic acid-responsive elements (SARE), TCA-element and TCA. CREs related to gibberellic acid are classified in class 5 and encompass GA response element (GARE-motif), TATC-box as well as P-Box. Last, The class pertains to ethylene hormone (ETH) and encompasses ethylene-responsive elements (ERE). The findings suggest that these proteins are likewise stimulated by hormonal changes and influence these pathways, resulting in corresponding reactions. The existence of these 21 regulatory components implies their activation and involvement in pathways controlled by hormones like auxin, abscisic acid, and others Supplementary Fig. 5.

The detected development-related responsive elements include another rearranged sequence: CGGTCC-box, AC-II, AC-I, HD-zip 3, HD-zip 1, CARE, circadian, re2f1, as-I, dOCT, AAGAA-motif, MSA like CAT-box, CCGTCC-box, GCN4-motif, E2Fb, NON, O2 Site, F-box, making a total of 20 elements altogether. The influence of these variables on cellular development is substantial, particularly in relation to cell cycle regulation and the processes that govern cellular proliferation. The AAGAA motif and as- represent the most common DREs. Some genes might be regulating circadian pathways as well as the mechanisms linked to zein metabolism. The observed patterns indicate a potential function in the tissue-specific expression of genes that are integral to the developmental process Supplementary Fig. 6.

These regulatory elements are necessary for activating genes that are involved in activating transcription factors like WRKY, etc. Their presence in the upstream regions of CqUSP genes indicates that these genes might get activated in response to biotic stress. Among 100 sequences, Four components linked to biotic stress were shown to be involved in wound healing and pathogen defence. Identified motifs include WRE-3, Box S, WUN-motif and W-box. WRE-3 and W-box are the most abundant regulatory elements found Supplementary Fig. 7.

As proven from previous studies, these genes get activated in response to abiotic stress stimulus, so the presence of these elements is necessary for the constitutive activation of the genes. The low-temperature response, also known as the response to cold, is characterised by LTR; other than that, the GC motif, DRE core, DRE-1, and CCAAT-box are drought-responsive elements. Additionally implicated are MBS-1, MBS, and MYB, as well as their binding and recognition sites. Like the site, MYC and MYB behave similarly. STRE causes low pH and osmotic pressure; additional causes include ARE and AT-rich sequences Supplementary Fig. 8.

The final class contains the nameless, unidentified sequences found in large excess but with no known function. In Unnamed__4, CTCC was the most eminent motif sequence, but other nameless regulatory motifs were also found Supplementary Fig. 9.

Prediction of putative microRNA target sites

Small, non-coding RNA molecules known as microRNAs (miRNAs) control the expression of genes by attaching to complementary sequences on target messenger RNA (mRNA) and causing translation to be inhibited or degraded. This post-transcriptional regulation is crucial in various biological processes, including development, differentiation, and stress responses. Upon analysis, 64 different miRNAs were predicted on 17/41 CqUSP genes. 29% of predicted miRNA targets inhibit using cleaving at specific target sites, whereas 71% cause inhibition on translation machinery. A detailed description of the target sites and specific miRNA is provided in Supplementary Table S5.

Identification of key glycosylation and phosphorylation sites in CqUSP proteins

The folding confers features and functions upon proteins and contributes to the stability of these protein structures through glycosylation. Sequences with potential signal peptides can be exposed to N-glycosylation machinery. In 41 CqUSp genes, variable numbers of glycosylation signals present range from as low as 1 to as high as 32 in AUR62037323, AUR62036292, and AUR62009857, respectively.

One important post-translational change affecting how biological pathways are activated, deactivated, and regulated is phosphorylation. During this process, the amino acids of serine, threonine, and tyrosine are phosphorylated by protein kinases. The phosphorylation sites varied in each transcript. In 41 putative protein sequences, these sites ranged from 7 to 104 in AUR62036940 and AUR62009857. The details of both are provided in Supplementary Tables 6 and 7.

Expression profiles of putative CqUSP genes

Upon analysis and filtering of the transcriptome data, it was revealed that all 41 Genes were present. Supplementary Table 8. Only 3 gave 0 expression; the rest were expressed in shoot leaves and root tissues. The highly expressed genes were AUR62024664, AUR62011820, AUR62033121, AUR62029290, AUR62008647, AUR62019037 and AUR6200172 Fig. 8.

Relative expression values of the CqUSPs in leaves and roots screened from transcriptomic data available on NCBI.

Integrated analysis of protein structure, disorder, and binding Sites in CqUSP proteins

The secondary structures were predicted for all four models. AUR62016751 contains 42.95% a-helices; extended strands constitute about 20.81% of the total protein, 2.68% turns, and random coils are about 33.56%. AUR62033121 contains 37.50%, 17.24%, 3,02%, and 42.24%, respectively. AUR62007707 contitutes about 27.57%, 11.35%, 4.09%, 56.99%. AUR62039147 have 25.09%, 17.22%, 6.41%, and 51.28 respectively. Supplementary Table 9. Disordered regions in proteins, or intrinsically disordered regions (IDRs), provide functional flexibility and adaptability, enabling proteins to interact with various partners and participate in multiple processes. They play crucial roles in regulation, signalling, and molecular recognition. These proteins were also checked for their disordered regions were also checked. AUR62016751, with 149 amino acid length disordered regions, is in the 1–35 region. The negative polyelectrolyte region in the protein is from 1 to 10 amino acids, and the polyampholyte region is from amino acids 25–35. The other three do not have disordered regions, according to the MobiDB webserver.

The protein models were generated using Swiss modelling, and the structure of the four representatives was generated Supplementary Fig. 10. The structural assessment profile of models and their resultant pictures are provided in Supplementary Table 10. Binding pockets were predicted for all four models. The catalytic or active pocket contains essential amino acids, details of which are provided in Supplementary Table 11. The presence of serine, threonine, and tyrosine residues confirmed the phosphorylation targets. In contrast, asparagine within binding pockets indicated that these genes contain glycosylation signals as well and will be exposed to both glycosylation and phosphorylation machinery for post-translational modifications.

Protein–protein interaction network

A few genes from the identified set were used to predict the interactions of these CqUSPs. STRING software was used to predict ten interactors for each protein. The complete STRING network depicts protein functional relationships; coloured lines indicate the type of interaction. AUR62016751 is a CqUSP gene that contains a single USP domain; the interacting partners of the genes are AUR62000481, a Proteolipid membrane potential modulator pmp three family protein. It works by adjusting the membrane potential, especially in resistance to elevated concentrations of cellular cations. Stress-activated mitogen-activated protein kinases are essential for relaying environmental cues to eukaryotic organisms that control gene expression and enable cells to respond to cellular stress. AUR62005541 and AUR62024193 contain RGS DOMAIN, which is a regulator of G protein signalling involved in GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways. AUR62005705 is a 50kDa subunit of the snRNA-activating protein complex, referred to as SNAP50 or subunit 3, plays a crucial role in activating RNA polymerases II and III within the complex. The structure includes a cysteine-histidine cluster featuring two potential zinc finger motifs.; AUR62013115 is a phosphoribosylformylglycinamidine cyclo-ligase, a chloroplastic protein involved in purine metabolism. AUR62013353 is an SPX DOMAIN containing protein involved in the cellular processes in response to phosphorous starvation., AUR62014305 is a DNA gyrase/topoisomerase involved in the supercoiling of the DNA strands, and the interaction of USP with this might help play a role in protecting DNA from external stresses; AUR62020281 is a Guanine nucleotide-binding protein alpha-1 subunit which plays its role in as modulators or transducers in various transmembrane signalling systems, AUR62037111 and AUR62042876 are nuclear redox-sensitive regulators and oxidative stress sensors Fig. 9.

PPI of protein with the CqUSP AUR62016751 single USP domain.

2nd representative chosen was an AUR62033121, which contains 2 USP domains. The STRING annotations show that it performs functions such as rRNA (pseudouridine) methyltransferase activity, Voltage-gated anion channel activity.its positive regulation of response to salt stress, regulation of RNA splicing along 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity, proton antiporter activity, and WD repeat are mostly uncharacterised. The interactive network showed that it interacts with AUR62001174, isoleucine–tRNA ligase, and is involved in the isoleucyl-tRNA aminoacylation; AUR62003624 is a BOLA2, which has a chaperone activity as well as works as maintaining cellular ion homeostasis, AUR62004134, AUR62013697 belongs to alpha/beta-Hydrolases superfamily proteins. It has a role in maintaining cellular homeostasis; AUR62011951 is a V-type proton ATPase subunit F. It has multiple subunits termed V1 and V0; the former is a peripheral complex that hydrolszes ATP. In contrast, the latter is connected to the membrane and is involved in proton translocation. V-type ATPases maintain the acidic environment and regulate the pH of cellular compartments. AUR62026042 is a protein N-terminal glutamine amidohydrolase and is involved in biological processes such as stress response, defence mechanisms against biotic stimuli and bacteria, and regulation of metabolic and biosynthetic pathways. These processes include the positive regulation of nitrogen and sulfur metabolism, secondary metabolite and phytoalexin biosynthesis, and cellular and biosynthetic activities. Catalytic activities include protein-N-terminal asparagine amidohydrolase, phosphorylase kinase regulator, and various hydrolase functions. These activities occur within intracellular anatomical structures, including the nucleus, cytoplasm, and organelles. Additionally, the processes involve interactions between organisms, protein oxidation, ubiquitin-dependent protein catabolism, and responses to ethylene-activated signalling pathways. AUR62036292, AUR62037072, AUR62038408, and AUR62036293 are USPA domain-containing proteins. This shows that CqUSPs interact with other proteins and members of their own gene family Fig. 10.

PPI of protein with the CqUSP AUR62033121 two USP domains.

The 3rd protein for which the interactions were checked belongs to the group containing the USP domain and a protein kinase domain. AUR62003991 and AUR62040255 are N-acetyltransferase domain-containing proteins involved in the transfer of acetyl groups from acetyl-CoA to various substrates. AUR62007241 and AUR62018759 are RING-type domain-containing proteins. These proteins function primarily as E3 ubiquitin ligases, facilitating the transfer of ubiquitin from E2 ubiquitin-conjugating enzymes to target substrates. This ubiquitination process regulates various cellular activities, which include the degradation of protein, signalling, and DNA repair mechanism, by marking proteins for proteasomal degradation or altering their cellular localszation and activity. AUR62008690 and AUR62025554 are pectinesterases and are involved in Glycan metabolism and pectin degradation. They catalyse the demethylation of pectin into pectate and methanol. Their fundamental role is in cell wall modification and degradation, impacting processes like plant growth, fruit ripening, and defence against pathogens by altering the rigidity and porosity of the cell wall. AUR62041410 is a CG-1 domain-containing protein and involves calmodulin binding. CG-1 domain-containing proteins are a class of proteins characterised by a CG-1 domain, typically involved in DNA binding. These proteins have key functional activities in the regulation of gene expression, particularly development, differentiation, and responses to environmental stimuli in plants Fig. 11.

PPI of protein with the CqUSP AUR62007707 having USP domain and protein kinase doamin.

The 4th protein, AUR62039147, which was only 1, contains a USP domain and, along with it, also has a pyr_redox domain. It interacts with AUR62000231, AUR62004128, and AUR62006577, is a cysteine desulfurase, and plays a key role in metabolic reactions that include sulfur, cysteine, and selenium compound metabolism as well. It plays a critical role in sulfurtransferase activity, iron-sulfur cluster assembly, and showing response against oxidative stress. Additionally, this enzyme is essential in the cellular amino acid metabolic process and in maintaining cellular redox homeostasis. AUR62007054 and AUR62019918 are Methionine gamma-lyase. It is an enzyme involved in metabolising sulfur-containing amino acids, specifically methionine and cysteine. It catalyses the breakdown of methionine into methanethiol, ammonia, and alpha-ketobutyrate. This enzyme plays a crucial role in sulfur amino acid catabolic and biosynthetic processes and cellular responses to various stimuli such as stress and nutrient levels. It is important for maintaining cellular amino acid homeostasis and metabolic pathways. AUR62008202 is present in the mitochondrial matrix and is involved in intracellular iron ion homeostasis; AUR62009179 is a tryptophanyl-tRNA synthetase, is an enzyme that attaches the amino acid tryptophan to its corresponding tRNA molecule. This process is essential for the accurate translation of genetic information into proteins. This enzyme also participates in cellular amino acid and nitrogen compound metabolism, playing a vital role in gene expression and protein biosynthesis. Additionally, it binds ATP and various other molecules necessary for its catalytic activity. AUR62017694 is an arginine–tRNA ligase. It is involved in arginyl-tRNA aminoacylation; AUR62026055 is thioredoxin-disulfide reductase (NADPH) activity and responses to reactive oxygen species, oxidative stress, and toxic substances, with involvement in various metabolic and catabolic pathways. These pathways regulate the biosynthesis of carbohydrates, macromolecules, and polysaccharides, detoxifying superoxide radicals and hydrogen peroxide and ensuring cellular homeostasis and redox balance. Key activities include thioredoxin-disulfide reductase, protein-disulfide reductase, and diverse oxidoreductase functions. These processes occur within cellular structures such as the cytoplasm, chloroplasts, and other organelles, playing pivotal roles in cellular responses and metabolic regulation. AUR62029200 is an. It also plays a role in developmental functions such as post-embryonic and flower development Fig. 12. Other members of the CqUSP gene family were also scanned for the interaction partners. The study reveals that along with the above-described proteins, they also interact with proteins mentioned in Table 1.

PPI of protein with the CqUSP AUR62039147 having USP domain and pyr_redox domain.