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At least 1,135 records · Page 63Linked to original sources
PubMed1998

Chemokine homolog of molluscum contagiosum virus: sequence conservation and expression.

An analysis of the complete Molluscum contagiosum virus (MCV-1) genome sequence revealed a 104-amino-acid open reading frame (MC148R) that is structurally related to the beta (CC) family of chemokines. The predicted MCV chemokine homolog (MCCH) has a deletion in the NH2-terminal activation domain, suggesting the absence of chemoattractant activity. The principal objectives of the present study were to determine whether: (i) MCCH is conserved in independent isolates of MCV-1 and MCV-2; (ii) MCCH mRNA is expressed in vivo; and (iii) the MCCH protein is secreted from mammalian cells. The nucleotide sequence of the MCCH gene locus was determined for 27 isolates of MCV-1 and 2 of MCV-2 obtained from 29 MCV-infected individuals. In each case, the characteristic CC sequence, the NH2-terminal deletion, and the length of the open reading frame were conserved, although there were some, mostly conservative, amino acid substitutions. Since MCV cannot be propagated in cell culture, mRNA was synthesized in vitro by the early transcription apparatus in purified MCV virions. MCCH RNA was amplified by RT-PCR; the sequence included the complete open reading frame and extended 40 to 50 nucleotides past the first poxviral termination signal (TTTTTNT). Similar RT-PCR results were obtained using total cellular RNA derived from MCV-infected tissue specimens. Finally, the MCCH open reading frame was expressed in a vaccinia virus vector and the predicted size polypeptide was secreted into the medium, as determined by Western blotting. Taken together, our data support the prediction that MCV expresses a secreted chemokine homolog that could antagonize the inflammatory response in vivo.

Amino Acid Sequence↗
PubMed2002

Discovery of five conserved beta -defensin gene clusters using a computational search strategy.

The innate immune system includes antimicrobial peptides that protect multicellular organisms from a diverse spectrum of microorganisms. beta-Defensins comprise one important family of mammalian antimicrobial peptides. The annotation of the human genome fails to reveal the expected diversity, and a recent query of the draft sequence with the blast search engine found only one new beta-defensin gene (DEFB3). To define better the beta-defensin gene family, we adopted a genomics approach that uses hmmer, a computational search tool based on hidden Markov models, in combination with blast. This strategy identified 28 new human and 43 new mouse beta-defensin genes in five syntenic chromosomal regions. Within each syntenic cluster, the gene sequences and organization were similar, suggesting each cluster pair arose from a common ancestor and was retained because of conserved functions. Preliminary analysis indicates that at least 26 of the predicted genes are transcribed. These results demonstrate the value of a genomewide search strategy to identify genes with conserved structural motifs. Discovery of these genes represents a new starting point for exploring the role of beta-defensins in innate immunity.

Amino Acid Motifs↗
PubMed2003

A participatory approach to ecosystem conservation: fuzzy cognitive maps and stakeholder group analysis in Uluabat Lake, Turkey.

Fuzzy cognitive mapping was used to develop a participatory ecosystem management plan for Uluabat Lake, Turkey. Interviews were conducted with stakeholders belonging to six different groups. Lake pollution was the most central and most mentioned variable for stakeholders. Stakeholder groups agree that lake pollution is negatively affecting ecosystem health and thereby local economies. Thus, reducing lake pollution was chosen as the overall goal for the management plan. Possible ways to reduce lake pollution and increase ecosystem health were seen differently by the different groups. Hunters, factory managers, NGO personnel, and local people thought industry was the main cause of lake pollution, while officials from the government and local municipalities thought roads and urban development contributed the most to lake pollution. Generally the stakeholder groups did not perceive their own actions as affecting the lake as strongly as other groups thought. For example, factory managers viewed factory pollution as negatively affecting the lake but less strongly than the other groups did. According to policy option simulations, reducing lake pollution had positive effects on all variables, especially fish, birds, animal husbandry, irrigation, agriculture, and the ecological balance of the lake. Results of this analysis were used to facilitate meetings among stakeholder groups and to develop a participatory ecosystem management plan. The analysis was useful for pointing out the similarities as well as the differences among the groups. It also helped the facilitators understand the focus of each stakeholder group and enabled them to suggest activities in which each group would want to participate.

Conservation of Natural Resources↗
PubMed2004

Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families.

MOTIVATION: Most proteins have evolved to perform specific functions that are dependent on the adoption of well-defined three-dimensional (3D) structures. Specific patterns of conserved residues in amino acid sequences of divergently evolved proteins are frequently observed; these may reflect evolutionary restraints arising both from the need to maintain tertiary structure and the requirement to conserve residues more directly involved in function. Databases of such sequence patterns are valuable in identifying distant homologues, in predicting function and in the study of evolution. RESULTS: A fully automated database of protein sequence patterns, Functional Protein Sequence Pattern Database (FPSPD), has been derived from the analysis of the conserved residues that are predicted to be functional in structurally aligned homologous families in the HOMSTRAD database. Environment-dependent substitution tables, evolutionary trace analysis, solvent accessibility calculations and 3D-structures were used to obtain the FPSPD. The method yielded 3584 patterns that are considered functional and 3049 patterns that are probably functional. FPSPD could be useful for assigning a protein to a homologous superfamily and thereby providing clues about function. AVAILABILITY: FPSPD is available at http://www-cryst.bioc.cam.ac.uk/~fpspd/

Algorithms↗
PubMed1998

Functional analysis of combinatorial mutants altered in a conserved region in loop E of the CP47 protein in Synechocystis sp. PCC 6803.

Regions in the large lumenally exposed region (loop E) of CP47 affect properties of the watersplitting system in photosystem II (PS II). To investigate the role of these regions, we developed a method for functional complementation of obligate photoheterotrophic mutants carrying a deletion in one such region. Using an obligate photoheterotrophic mutant that carries a short deletion (delta (D440-P447) in loop E of CP47, completely degenerate sequences of eight codons in length were introduced at the site of the deletion. Transformants that were complemented to photoautotrophic growth were selected, and 20 such mutants were studied. Sequence analysis revealed that, as expected, in each of them CP47 had been restored to its wild-type length. However, none of the amino acid residues in the deleted region were found to be critical for function. A negatively charged residue at position 440 and a positively charged one at position 444 were favored but not required. Photoautotrophic growth of mutants obtained varied from almost normal to significantly impaired. The mutants contained 20-100% of the amount of PS II present in the wild type, with PS II amounts correlating with the initial rates of oxygen evolution. The mutants had a high rate of photoinactivation, and many mutants showed an up to 1000-fold increase in chloride requirement for photoautotrophic growth. These phenotypic effects were a direct consequence of the CP47 mutations and were not caused by altered binding of one of the extrinsic proteins. No particular amino acid residues in positions 440-447 of CP47 were found to be indispensable for photoautotrophic growth, and many amino acid combinations in this region support PS II function. However, the mutagenized region is shown to interact with the oxygen-evolving site of PS II and appears to have a direct role in chloride binding.

Bacterial Proteins↗
PubMed2004

[Fertility of women after conservative operation for borderline ovarian tumors].

OBJECTIVES: The aim of the study was to assess procreation in group of patients who were treated by conservative operation for borderline tumors of the ovary. DESIGN: The analysis included 42 patients conservatively operated for ovarian tumor of borderline malignancy in Department of Gynecology Medical University of Gdansk between 1978-2000. The incidence of pregnancy, age of patients, tumor pathology, type of conservative surgery and the course of pregnancy and labour were evaluated in this study. RESULTS: In the analysis group were 36 (85.7%) stage IA, 2 (4.8%) stage IB, 3 (7.1%) stage IC and 1 (2.4%) stage III C patients. Unilateral adnexectomy was performed in 36 (85.7%) patients, 4 (9.5%) unilateral cystectomy, 2 (4.8%) bilateral cystectomy with omentectomy in one case. After conservative operation 10 (23.8%) patients were pregnant and delivered healthy children but 2 patients delivered twice and 1 third. Recurrence was observed in 2 patients in period of 27 and 50 months after operation. 5 years survival was 97.6%. CONCLUSIONS: Percentage of pregnancy after conservative treatment for borderline ovarian tumors was high (23,8%) and number of recurrences was low so conservative surgery allows young women to retain procreational potential without increasing risk of recurrence.

Adult↗
PubMed2000

Phylogeny of the serpin superfamily: implications of patterns of amino acid conservation for structure and function.

We present a comprehensive alignment and phylogenetic analysis of the serpins, a superfamily of proteins with known members in higher animals, nematodes, insects, plants, and viruses. We analyze, compare, and classify 219 proteins representative of eight major and eight minor subfamilies, using a novel technique of consensus analysis. Patterns of sequence conservation characterize the family as a whole, with a clear relationship to the mechanism of function. Variations of these patterns within phylogenetically distinct groups can be correlated with the divergence of structure and function. The goals of this work are to provide a carefully curated alignment of serpin sequences, to describe patterns of conservation and divergence, and to derive a phylogenetic tree expressing the relationships among the members of this family. We extend earlier studies by Huber and Carrell as well as by Marshall, after whose publication the serpin family has grown functionally, taxonomically, and structurally. We used gene and protein sequence data, crystal structures, and chromosomal location where available. The results illuminate structure-function relationships in serpins, suggesting roles for conserved residues in the mechanism of conformational change. The phylogeny provides a rational evolutionary framework to classify serpins and enables identification of conserved amino acids. Patterns of conservation also provide an initial point of comparison for genes identified by the various genome projects. New homologs emerging from sequencing projects can either take their place within the current classification or, if necessary, extend it.

Amino Acid Sequence↗
PubMed2025

Genetic Conservation and Diversity of SARS-CoV-2 Envelope Gene Across Variants of Concern.

SARS-CoV-2 Envelope (E) protein is critical in viral assembly, release, and virulence. E gene was considered highly conserved and evolving slowly. Pan-sarbecoviruses-conserved regions in the E gene have been used as targets for various RT-PCR assays to detect SARS-CoV-2. It remains elusive whether SARS-CoV-2 variants of concern (VOCs) have accumulated significant E mutations that may affect protein stability and diagnostic RT-PCR assays. Herein we aimed to perform a comprehensive genetic analysis on the conservation and diversity of the E gene of SARS-CoV-2 and its VOCs in comparison with other human coronaviruses (HCoVs). In silico analysis of 20 326 HCoV E gene sequences retrieved from GenBank and GISAID suggests that SARS-CoV-2 E gene has multiple pan-HCoVs- and pan-SARS-CoV-2-conserved positions but accumulates significant mutations in VOC B.1.351 and Omicron strains. Mutations were often found in the 5' and 3' variable regions, whereas the central region is conserved. Nucleotide changes C109U and A114G may lead to potential failure of first-line SARS-CoV-2 diagnostic/screening assays. Nucleotide change C212U and its concomitant amino acid substitution Pro71Leu (i.e., C212U/Pro71Leu) is a hallmark mutation of B.1.351 variants, while C26U/Thr9Ile is characteristic of all Omicron variants. Later Omicron subvariants, such as XBB.1.5 and EG.5, additionally acquired the A31G/Thr11Ala mutation, as was confirmed by whole genome sequencing of SARS-CoV-2 in 118 pediatric cases. Wild-type E protein exhibits cytotoxicity to cells, but the mutations Thr9Ile, Thr11Ala, Thr9Ile + Thr11Ala, or Pro71Leu reduces its cytotoxicity. The Thr9Ile + Thr11Ala mutation stabilizes the E proteins of Omicron variants, while Pro71Leu alters the cellular distribution of the E protein, reducing its colocalization with the Golgi body. Altogether, this study not only sheds light on the conservation and diversity of the E gene in SARS-CoV-2 and its VOCs but also informs the improvement and development of SARS-CoV-2 or pan-HCoVs screening and diagnostic assays.

SARS-CoV-2↗
PubMed2006

[Comparative retrospective analysis of pain afflictions in patients with lumbar discopathy receiving conservative or operative therapies].

UNLABELLED: Pain afflictions are the basic problems in patients with discopathy of the lumbar backbone. Pain control is the key therapeutic task in patients with a disease of the intervertebral disc. Degree of reduction of the pain sensations is one of the most important criteria in assessment of the treatment efficacy. THE AIM: of this study was to evaluate the pain afflictions in patients with lumbar discopathy treated with conservative and operative therapies. MATERIAL AND METHODS: 665 patients aged between 16 and 76 years with discopathy at L4-L5 and L5-S1 levels have been enrolled to the study. In estimated group 348 patients received only a conservative therapy whereas 317 patients undergone an operative procedure. Analysis has been performed based on pain rating scores: Low Back Pain Rating Scale (LBPRS), Japanese Orthopedic Association Low Back Pain Score (JOA-LBPS), Domial's pain rating score. RESULTS: Results of performed studies show that conservative and operative treatment significantly alleviate pain affliction in patients with lumbar discopathy. Complete abatement of pain afflictions more frequent refers to operated patients than those only receiving conservative therapy. Alleviation of pain afflictions within a period of three years following operating procedure is significantly higher than within analogous period of conservative treatment. Reduction of pain obtained as a result of surgical procedure in higher degree refers to limb than backbone. Treatment method does not exert an influence on nature of pain afflictions within distant period. CONCLUSIONS: Alleviation of pain afflictions within a period of three years following operating procedure is significantly higher than within analogous period of conservative treatment. Treatment method does not exert an influence on nature of pain afflictions within distant period. Patients at the age of above 50 notify the higher level of intensity of pain ailments than young patients and patients in mid age.

Adolescent↗
PubMed2026

Structure-informed theoretical modeling defines principles governing avidity in bivalent protein interactions.

In signaling cascades, signaling proteins often encode multiple domains or motifs, which presents the possibility for avidity -- where multivalent binding drastically increases interaction strength and duration. However, predicting and validating multivalent interactions that interact with avidity is a challenge. Here, we integrate mechanistic modeling, structure-based analysis, and experimental approaches as a framework for defining the conditions under which avidity plays a role. We explore the tandem SH2 domain family of interactions with bisphosphorylated partners as a multivalent archetype, which encompasses key secondary messengers in tyrosine kinase signaling networks. Theoretical modeling suggests that maximum avidity occurs with closely spaced tyrosine phosphorylation sites combined with moderate monovalent affinities - exactly around the innate range of SH2 domain affinity - or with phosphorylation sites separated by sufficiently flexible linkers. Surprisingly, despite sequence diversity, structure-based analysis showed relatively conserved three-dimensional spacing between SH2 domains across all tandem SH2 families, which we corroborate experimentally, suggesting evolutionary optimization for avidity interactions. The combination of structure-based analysis of domain spacing with available monovalent experimental data appears, along with iterative experimental refinement of biophysical parameters, can identify high affinity interactions of tandem SH2 domain recruitment to the EGFR C-terminal tail. Using these principles, we extended bivalent predictions into the full phosphoproteome space and structural parameterization of other partners of SH2 domain binding, providing resources and methods for more rapid expansion of bivalent analysis. These approaches lay the groundwork for larger utility in multivalent prediction and testing to help better understand protein interactions that drive cell signaling.

BLI↗
PubMed1996

Human pseudoautosomal boundary-like sequences: expression and involvement in evolutionary formation of the present-day pseudoautosomal boundary of human sex chromosomes.

The human genome is composed of long-range mosaic structures of G+C% (GC%), which are thought to be related to chromosome bands. We previously identified a boundary of Mb-level domains of GC% mosaic structures in the human major histocompatibility complex (MHC) and found in the domain boundary a sequence very similar to pseudoautosomal boundary (PAB) sequences of human sex chromosomes. We designated it 'PABL' and found many PABLs in the human genome. By analysis of six genomic and six transcribed PABLs, a core and consensus sequence of about 650 nt was defined; the 3'- and 5'-edges of the PABLs were strictly conserved. Northern blot analysis showed sizes of PABL transcripts to be 5-10 kb in length. Divergence time of PABLs was estimated to be 60-120 million years ago by analysis of human PABLs and PABXY1 of seven primates, and the evolutionary rates deduced showed PABLs to have been under selective constraints. A model for evolutionary formation of the present pseudoautosomal boundary was proposed by postulation of illegitimate recombination between two PABLs.

Animals↗
PubMed2025

Structure-informed theoretical modeling defines principles governing avidity in bivalent protein interactions.

In signaling cascades, where domain-motif interactions tend to interact with relatively low affinity (allowing for reversibility), signaling proteins often encode multiple domains or motifs, which present the possibility of avidity - drastically increasing the interaction strength and duration as a result of multivalent binding. However, given the large combinatorial space, predicting and validating multivalent interactions that interact with avidity is a challenge. Here, we integrate mechanistic modeling, structure-based analysis, and experimental approaches as a framework for defining the conditions under which avidity plays a role. We explore the tandem SH2 domain family of interactions with bisphosphorylated partners as a multivalent archetype, which encompasses key secondary messengers in tyrosine kinase signaling networks. While certain multivalent interactions have been shown to be necessary in immune receptor recruitment of partners, bivalent recruitment of tandem SH2 domains more broadly is poorly understood. Theoretical modeling suggests that maximum avidity occurs with closely spaced or flexibly linked phosphotyrosine sites, combined with moderate monovalent affinities - exactly around the innate range of SH2 domain affinity. Surprisingly, despite sequence diversity, structure-based analysis showed remarkably conserved three-dimensional spacing between SH2 domains across all tandem SH2 families, which we corroborate experimentally, suggesting evolutionary optimization for avidity interactions. The combination of structure-based analysis of domain spacing with available monovalent experimental data appears to be sufficiently accurate to predict and rank order high affinity interactions of tandem SH2 domain recruitment to the EGFR C-terminal tail. These approaches lay the groundwork for larger utility in multivalent prediction and testing to help better understand protein interactions that drive cell signaling.

BLI↗
PubMed2005

Expression and functional analyses of mHAUSP regulating apoptosis of cervical adenocarcinoma cells.

p53 tumor suppressor protein is stabilized by the herpes-virus-associated ubiquitin-specific protease (HAUSP), a deubiquitinating enzyme. We previously isolated a mouse orthologue of HAUSP, mHAUSP, encoding 1103 amino acids with a molecular weight of approximately 135 kDa containing highly conserved Cys, Asp (I), His, and Asn/Asp (II) domains. In this study, we investigated the temporal and spatial expression of mHAUSP during the early mouse embryonic development. Northern blot analysis revealed that the expression of mHAUSP was detected throughout the process of embryonic development with the maximal expression between E10.5 and E13.5. In situ hybridization study showed the global expression of mHAUSP in various organs of embryos, including mesencephalon, spinal cord, lung and genital eminence. In addition, we carried out biochemical analysis for 6 conserved amino acids (Cys224, Gln231, Asp296, His457, His465, and Asp482) in Cys box, QQD box, and His box in order to investigate their structural and functional roles of these amino acid residues. The conserved Gln231 was not essential for the catalytic activity of mHAUSP. However, other conserved amino acids were required for deubiquitinating enzyme activity of mHAUSP. Moreover, we observed that the overexpression of mHAUSP induces cell death in HeLa cells.

Amino Acid Sequence↗
PubMed1998

Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: conserved gene order among octocorals.

The nucleotide sequence for an 11,715-bp segment of the mitochondrial genome of the octocoral Sarcophyton glaucum is presented, completing the analysis of the entire genome for this anthozoan member of the phylum Cnidaria. The genome contained the same 13 protein-coding and 2 ribosomal RNA genes as in other animals. However, it also included an unusual mismatch repair gene homologue reported previously and codes for only a single tRNA gene. Intermediate in length compared to two other cnidarians (17,443 and 18,911 bp), this organellar genome contained the smallest amount of noncoding DNA (428, compared to 1283 and 781 nt, respectively), making it the most compact one found for the phylum to date. The mitochondrial genes of S. glaucum exhibited an identical arrangement to that found in another octocoral, Renilla kolikeri, with five protein-coding genes in the same order as has been found in insect and vertebrate mitochondrial genomes. Although gene order appears to be highly conserved among octocorals, compared to the hexacoral, Metridium senile, few similarities were found. Like other metazoan mitochondrial genomes, the A + T composition was elevated and a general bias against codons ending in G or C was observed. However, an exception to this was the infrequent use of TGA compared to TGG to code for tryptophan. This divergent codon bias is unusual but appears to be a conserved feature among two rather distantly related anthozoans.

Amino Acid Sequence↗
PubMed2004

Molecular evolution of epididymal lipocalin genes localized on mouse chromosome 2.

We previously identified two murine secretory proteins, mE-RABP(Lcn5) and mEP17(Lcn8), belonging to the lipocalin family and specifically expressed in the epididymis. The genes are contiguous and localized on mouse chromosome 2. We now show that five other related lipocalin genes, Lcn9, Lcn10, Lcn11, Lcn12, and Lcn13, that evolved by in situ tandem duplication are present on the same locus. Lcn9, Lcn10, Lcn12, and Lcn13 genes, like Lcn5 and Lcn8 genes, are specifically expressed in the mouse epididymis. However, each gene has a distinct spatial expression within the epididymis and different regulation. Analysis of the human genome sequence shows the presence of genes encoding lipocalins with genomic organization, chromosomal arrangement, and orientation similar to that of the corresponding murine genes, indicating that the epididymal cluster is evolutionary conserved. A phylogenetic analysis of the new epididymal proteins reveals their spread position in the lipocalin protein family tree. This suggests the preservation of the regulatory sequences, while protein sequences have greatly diverged, reflecting functional diversity and possibly multifunctionality. In terms of the cluster ancestry, epididymal expression possibly appeared in a PGDS-like lipocalin in amniotes, and the duplications generating the cluster occurred at least in the common ancestor of rodents and primates. The presence and conservation of a cluster of five genes encoding epididymal lipocalins, differently regulated and regionalized in the epididymis, strongly suggests that these proteins may play an important role for male fertility.

Acute-Phase Proteins↗
PubMed2004

Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription.

Pax6 is a transcription factor with an essential role in eye, central nervous system, and pancreas development. Its expression pattern is restricted to these specific domains within the developing embryo. Here four conserved elements are identified in Pax6 intron 7, showing a high level of sequence conservation between human, mouse, pufferfish, and zebrafish. Three of these are shown to act as cis-regulatory elements, directing expression of a reporter gene to distinct subsets of the Pax6 expression domain. CE1 regulates gene expression in late eye development, CE2 drives expression in the diencephalon and in the developing heart tube where Pax6 is not normally expressed, while CE3 directs expression in rhombencephalon. CE2 is shown to be autoregulated in the diencephalon, responding to absence of Pax6. We identify a highly conserved Pax6 recognition site and demonstrate its ability to bind Pax6 specifically. CE1 is embedded in a CpG island, and we identify a novel Pax6 transcript which initiates from this region. Functional analysis of evolutionary conserved sequences pinpoints novel cis-acting elements that govern the regulation of the complex spatio-temporal and quantitative expression of Pax6.

Alternative Splicing↗
PubMed2026

Genomic determinants underlying biogenic amine detoxification phenotypes in food-associated lactic acid bacteria: Mechanism, evolutionary origin, and relevance to fermented food safety.

Biogenic amines (BAs) are toxic metabolites that accumulate in fermented foods and pose significant food safety concerns. Although several lactic acid bacteria (LAB) have previously been reported to exhibit strain-specific BA-degrading phenotypes, the genetic determinants underlying these activities have remained largely uncharacterized. Here, we analyzed 8251 LAB genomes to validate BA-degrading phenotypes. We predicted five BA-associated genes, including two direct biogenic amine-degrading genes (BADGs), mco and patA, and three polyamine-modifying genes (PMGs), speG, paiA, and bltD. Among BADGs, mco was broadly distributed across LAB and strongly enriched across food-associated niches. patA, organized within a conserved potD-glnB-potABC-patA cassette, is a putative, functionally distinct BADG in LAB, revealing a nitrogen-responsive polyamine uptake-catabolism module. Phylogenomics, phylogenetic reconciliation, and synteny analysis established that all five genes entered the LAB through episodic horizontal gene transfer followed by lineage-specific fixation. GC compositional bias and mobile genetic element association further corroborated the horizontal origin of the two BADGs. Structural analysis confirmed the conservation of catalytic core residues of BADGs across LAB, indicating strong purifying selection. Phenotype-to-genotype correlation with experimentally reported LAB suggested mco as a reliable genomic predictor of degrading phenotype. Integration of degradation and biosynthetic profiles predicted multiple LAB species capable of both synthesizing and degrading BA, along with 1823 genomes with degradation potential but lacking detectable BA biosynthesis genes. This study provides the first large-scale genome framework linking BA-degrading phenotypes with their genetic determinants in LAB and offers a rational basis for selecting BA-detoxifying strains for fermented food applications.

Biogenic Amines↗
PubMed2026

Genome-wide identification of CXE gene family in soybean and functional characterization of GmCXE31 in lipid biosynthesis and salt tolerance.

GmCXE31 negatively regulates salt tolerance and lipid synthesis in soybean, and the cxe31-edited lines improve soybean yield and seed quality. Carboxylesterases (CXEs), as essential lipid hydrolases of the α/β-hydrolase fold superfamily, are critical for plant stress responses, hormone signaling and secondary metabolism. The key candidate gene GmCXE31 was previously identified in our laboratory through a genome‑wide association study (GWAS) of soybean lipid‑related traits. In the present study, we further identified 60 GmCXE family genes in soybean. Phylogenetic analysis clustered them into 11 conserved subfamilies. Cis-acting element analysis showed their promoters are enriched with elements related to abiotic stress, growth and hormone signaling, suggesting potential roles in soybean development and stress adaptation. GmCXE31 is highly expressed in seedling roots and responsive to strigolactones (SLs) and salt stress. Functional assays revealed that GmCXE31 negatively regulates soybean salt tolerance: its overexpression reduced salt tolerance in Arabidopsis and soybean under 150 mM NaCl stress, while its knockout enhanced this trait. Lipid profiling revealed GmCXE31-edited lines had higher seed oil content, elevated oleic/linoleic acid ratio and lower saturated fatty acid proportion, which was achieved by regulating lipid synthesis-related genes like GmNFYA. Agronomic trait analysis showed GmCXE31-edited lines had increased nodule number, plant height and single-plant yield at maturity, with opposite phenotypes in overexpression lines. In conclusion, this study elucidates the multifaceted roles of GmCXE31 in coordinating soybean salt tolerance, lipid metabolism and agronomic traits, providing theoretical and genetic resources for salt-tolerant and high-quality soybean molecular breeding.

Glycine max↗