Sunil Kumar Singh

Deg proteases are ATP-independent serine endopeptidases found in bacteria, archaea, and eukaryotes including plants. They are considered to be key regulators of development and stress tolerance in plants. In this study, a comprehensive genome-wide analysis identified 19 serine protease-like DEG family proteins in potato (Solanum tuberosum L.), revealing their structural diversity, domain architecture, and regulatory potential. Physiochemical profiling showed a predominance of acidic isoelectric points (pI), variable protein lengths (169–1083 amino acids), and differential stability indices. Subcellular localization predicted most DEG proteases to reside in the chloroplast, with others distributed across cytoplasm, nucleus, mitochondria, and peroxisome. Domain analysis confirmed the universal presence of the trypsin domain, with varying numbers of PDZ domains and additional conserved motifs among paralogs. Gene ontology annotations linked DEG proteases to key biological functions including PSII repair, photoinhibition, and chloroplast organization, alongside protein catabolism and light stimulus response. Promoter analysis revealed an abundance of cis-regulatory elements (CREs), particularly light-responsive motifs, along with hormone and stress-related elements such as ABRE, ARE, and MBS. Expression profiling across eight developmental tissues demonstrated tissue-specific expression patterns, with strong transcript accumulation of selected DEG members in senescent leaf, stolon, shoot apex, and tuber. Interestingly, several splice variants showed unique expression dynamics, including stage-specific and stress-induced activation. Upon exposure to abiotic and hormonal cues, 16 DEG proteases displayed significant transcriptional modulation, particularly under light, ABA, and Zeatin treatments, with notable fold changes reaching up to 26-fold in certain variants. These findings highlight the functional versatility of DEG proteases in potato development and stress adaptation, especially their responsiveness to light and hormonal stimuli. The characterization of these proteases paves the way for future studies on their roles in crop resilience and genome editing applications.

Neolamarckia cadamba is a fast-growing tropical hardwood tree that is used extensively for plywood and pulp production, light furniture fabrication, building materials, and as a raw material for the preparation of certain indigenous medicines. Lack of genomic resources hampers progress in the molecular breeding and genetic improvement of this multipurpose tree species. In this study, transcriptome profiling of differentiating stems was performed to understand N. cadamba xylogenesis. The N. cadamba transcriptome was sequenced using Illumina paired-end sequencing technology. This generated 42.49 G of raw data that was then de novo assembled into 55,432 UniGenes with a mean length of 803.2bp. Approximately 47.8% of the UniGenes (26,487) were annotated against publically available protein databases, among which 21,699 and 7,754 UniGenes were assigned to Gene Ontology categories (GO) and Clusters of Orthologous Groups (COG), respectively. 5,589 UniGenes could be mapped onto 116 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Among 6,202 UniGenes exhibiting differential expression during xylogenesis, 1,634 showed significantly higher levels of expression in the basal and middle stem segments compared to the apical stem segment. These genes included NAC and MYB transcription factors related to secondary cell wall biosynthesis, genes related to most metabolic steps of lignin biosynthesis, and CesA genes involved in cellulose biosynthesis. This study lays the foundation for further screening of key genes associated with xylogenesis in N. cadamba as well as enhancing our understanding of the mechanism of xylogenesis in fast-growing trees.

Summary: Arabidopsis IRX10 and IRX10‐LIKE (IRX10‐L) proteins are closely related members of the GT47 glycosyltransferase family. Single gene knock‐outs of IRX10 or IRX10‐L result in plants with either a weak or no mutant phenotype. However irx10 irx10‐L double mutants are severely affected in their development, with a reduced rosette size and infrequent formation of a small infertile inflorescence. Plants homozygous for irx10 and heterozygous for irx10‐L have an intermediate phenotype exhibiting a short inflorescence compared with the wild type, and an almost complete loss of fertility. Stem sections of the irx10 homozygous irx10‐L heterozygous or irx10 irx10‐L double mutants show decreased secondary cell‐wall formation. NMR analysis shows that signals derived from the reducing end structure of glucuronoxylan were detected in the irx10 single mutant, and in the irx10 homozygous irx10‐L heterozygous combination, but that the degree of polymerization of the xylan backbone was reduced compared with the wild type. Additionally, xylans from irx10 stem tissues have an almost complete loss of the GlcUA side chain, whereas the level of 4‐O‐Me‐GlcUA was similar to that in wild type. Deletion of the predicted signal peptide from the N terminus of IRX10 or IRX10‐L results in an inability to rescue the irx10 irx10‐L double mutant phenotype. These findings demonstrate that IRX10 and IRX10‐L perform a critical function in the synthesis of glucuronoxylan during secondary cell‐wall formation, and that this activity is associated with the formation of the xylan backbone structure. This contrasts with the proposed function of the tobacco NpGUT1, which is closely related to the Arabidopsis IRX10 and IRX10‐L proteins, in rhamnogalacturonan II biosynthesis.

Cell size and secondary cell wall patterning are crucial for the proper functioning of xylem vessel elements in the vascular tissues of plants. Through detailed anatomical characterization of Arabidopsis thaliana hypocotyls, we observed that mutations in the putative spermine biosynthetic gene ACL5 severely affected xylem specification: the xylem vessel elements of the acl5 mutant were small and mainly of the spiral type, and the normally predominant pitted vessels as well as the xylem fibers were completely missing. The cell-specific expression of ACL5 in the early developing vessel elements, as detected by in situ hybridization and reporter gene analyses, suggested that the observed xylem vessel defects were caused directly by the acl5 mutation. Exogenous spermine prolonged xylem element differentiation and stimulated cell expansion and cell wall elaboration in xylogenic cell cultures of Zinnia elegans, suggesting that ACL5 prevents premature death of the developing vessel elements to allow complete expansion and secondary cell wall patterning. This was further supported by our observations that the vessel elements of acl5 seemed to initiate the cell death program too early and that the xylem defects associated with acl5 could be largely phenocopied by induction of premature, diphtheria toxin-mediated cell death in the ACL5-expressing vessel elements. We therefore provide, for the first time, mechanistic evidence for the function of ACL5 in xylem specification through its action on the duration of xylem element differentiation.

Background: Formation of plant root hairs originating from epidermal cells involves selection of a polar initiation site and production of an initial hair bulge which requires local cell wall loosening. In Arabidopsis the polar initiation site is located towards the basal end of epidermal cells. However little is currently understood about the mechanism for the selection of the hair initiation site or the mechanism by which localised hair outgrowth is achieved. The Arabidopsis procuste1 (prc1-1) cellulose synthase mutant was studied in order to investigate the role of the cell wall loosening during the early stages of hair formation. Results: The prc1-1 mutant exhibits uncontrolled, preferential bulging of trichoblast cells coupled with mislocalised hair positioning. Combining the prc1-1 mutant with root hair defective6-1 (rhd6-1), which on its own is almost completely devoid of root hairs results in a significant restoration of root hair formation. The pEXPANSIN7::GFP (pEXP7::GFP) marker which is specifically expressed in trichoblast cell files of wild-type roots, is absent in the rhd6-1 mutant. However, pEXP7::GFP expression in the rhd6-1/prc1-1 double mutant is restored in a subset of epidermal cells which have either formed a root hair or exhibit a bulged phenotype consistent with a function for EXP7 during the early stages of hair formation. Conclusion: These results show that RHD6 acts upstream of the normal cell wall loosening event which involves EXP7 expression and that in the absence of a functional RHD6 the loosening and accompanying EXP7 expression is blocked. In the prc1-1 mutant background, the requirement for RHD6 during hair initiation is reduced which may result from a weaker cell wall structure mimicking the cell wall loosening events during hair formation.

Despite the importance of secondary growth in plants, relatively few genes regulating this process have been identified to date. By using data from detailed transcript profiling of the poplar wood‐forming tissues, 150 genes that are differentially expressed within the zone of secondary growth were identified. In order to determine the possible function of these poplar genes, potential Arabidopsis thaliana orthologs were identified and gene knockout lines analysed. Three selection filters were used to identify the most likely orthologous genes using poplar and Arabidopsis sequence comparisons, expression profiling in secondary thickened Arabidopsis hypocotyls and global expression analysis of Arabidopsis tissues. Three genes encoding AtCSLA2 (At5g22740), the AtGUT1 GT47 glycosyltransferase (At1g27440) and a protein with no proposed function AtUNKA (At4g27435) were selected for further detailed analysis of their role in secondary growth in Arabidopsis. The presented genome‐based approach using both poplar and Arabidopsis systems provides powerful means towards assigning biological functions to enzymes with poorly understood biochemical activity, such as AtCSLA2 and AtGUT1, as well as for proteins with no known function.