Biology subjects

Routray, P.

Publications and source records attributed to Routray, P..

10 recordsLinked to original sources

bioRxiv2026

Dose dependent impact of global Cc2d1a reduction on cognitive, social, and metabolic phenotypes

Background Autism spectrum disorder (ASD) and Intellectual disability (ID) share an in-creased male prevalence, but the biological mechanisms underlying this male bias remain poorly understood. Mice deficient for CC2D1A, a protein scaffold mutated in ASD/ID, have shown multiple male-specific deficits both in ASD-like behaviors and in the regulation of neuronal intracellular signaling pathways. However, previous re-search relied on conditional knockout (cKO) models due to early postnatal lethality of global Cc2d1a KO strains. Thus, the ability to define the developmental impacts of CC2D1A LOF in mice has been limited. While generating a Cc2d1a knock-in strain with V5-HA epitope tags, we found that homozygous animals (Cc2d1aVH/VH) resulted in a hypomorph line that can be used to study developmental loss of CC2D1A. Methods We assessed gross morphology, behavior, and intracellular signaling in male and female Cc2d1aVH/VH animals, where only ~20% of CC2D1A is present. We then crossed this line with a null allele to obtain a more severe hypomorph (Cc2d1a-/VH) and explore phenotypic penetrance thresholds. In addition to the previous phenotypic characterization, we also assessed body composition, feeding, and molecular hall-marks of metabolic function in both sexes. Results We found that ~80% CC2D1A reduction in Cc2d1aVH/VH mice did not recapitu-late any of the behavioral or molecular disruptions seen in cKO models. In contrast, ~90% CC2D1A reduction in Cc2d1a-/VH mice resulted in ASD/ID-like behavioral phe-notypes in males, similar to those reported in cKO lines, with distinct intracellular sig-naling disruptions. Male and female Cc2d1a-/VH mice also showed subtle but signifi-cant adult weight deficits associated with distinct metabolic changes. Limitations These models still do not fully recapitulate the complete CC2D1A LOF found in patients. Due to the analysis of two independent strains over multiple metrics, these studies are not powered to compare statistical differences between sexes and data were analyzed in males and females independently. Conclusions We identified a strikingly narrow CC2D1A expression threshold for the emer-gence of ASD/ID-like behavioral deficits in males. In addition, we revealed a novel role for CC2D1A in adult weight gain. These mouse strains will be useful to better under-stand CC2D1A LOF phenotypes.

neuroscience↗

bioRxiv2026

The chloroplast CLP chaperone-protease system controls the steady-state abundance of the singlet oxygen sensors EXCUTER 1 and 2

O_LIThe chloroplast CLP chaperone-protease is essential for chloroplast biogenesis. CLP substrate selection is aided by the N-recognin CLPS1 and CLPF adaptors. They interact with each other and the CLPC1 chaperone, but their specific functions are poorly understood. C_LIO_LIWe employed in vivo CLPC1 substrate-trapping in Arabidopsis by expressing a 35S:CLPC1-TRAP-STREPII transgene in wild-type (WT), clpf, clps1, and clpfclps1 to test the consequences of the loss of these adaptors on CLPC1-trapped proteins. Immunoblotting and protein half-life experiments were carried out for identified CLP substrates. C_LIO_LIExpression of the 35S:CLPC1-TRAP-STREPII in clps1cpf was embryo lethal. CLPF was trapped at a reduced level in clps1, supporting CLPS-CLPF interactions. Chloroplast 1O2 sensor EXECUTER1 (EX1) was trapped in WT and clps1 but not significantly in clpf. Steady-state protein accumulation of EX1 and its homolog EX2 increased 30-fold in the CLPC1-TRAP lines and clpr2-1, but not in clpf or clps1. In planta experiments showed that the half-life of EX1 is [~]3-fold longer in clpc1-1 than in WT, but EX1 half-life was unaffected in clpf. C_LIO_LIWe conclude that the CLP system plays a key role in EX1,2 homeostasis by keeping their intra-chloroplast concentrations low through continuous degradation, upstream of their 1O2 signaling function. C_LI

plant biology↗

bioRxiv2026

The chloroplast CLPD chaperone: consequences of under- and overexpression, interaction with the CLP protease core, and candidate substrates

Expression of the chloroplast AAA+ chaperone CLPD gene increases during senescence and drought, but its function in chloroplast proteostasis is poorly understood. This study provides a comprehensive analysis of Arabidopsis CLPD protein accumulation across development from early seedlings to senescence, and compares results to its homologs CLPC1,2, as well as CLPB3 and cpHSP90. The developmental consequences of complete loss of CLPD expression (clpd-1), as well as overexpression of functional CLPD or CLPD impaired in ATP hydrolysis (CLPD-TRAP), were determined in Arabidopsis. clpd-1 has accelerated seedling development while functional CLPD overexpression lines, but not CLPD-TRAP, have delayed development. To determine if CLPD is a bona fide CLP chaperone associating with the CLPPRT protease and to identify in vivo candidate substrates, we employed the CLPD-TRAP line during vegetative and flowering (senescent) growth stages. Affinity purification of CLPD-TRAP followed by mass spectrometry showed high enrichment of all nine subunits of the CLP protease, suggesting that CLPD plays a role in substrate delivery to the CLP protease. CLPC1,2 were also highly enriched in the CLPD-TRAP interactome, and together with prior information, suggesting hetero-oligomerization of the three chaperones. Nine chloroplast candidate substrates were identified in the CLPD-interactomes, including: FHY2 involved in riboflavin synthesis, THI1 and THIC involved in thiamin metabolism, and four proteins of unknown function. Several of these were previously identified as potential CLP substrates based on CLPC1 trapping and comparative proteomics of clp mutants. Together, this suggests that CLPD acts in substrate selection within a heteromeric CLPC-CLPD hexamer, likely with unique contributions.

plant biology↗

bioRxiv2026

Loss of Mitochondrial FMT Restores Chloroplast Proteostasis via Inter-organelle Compensation

Chloroplast proteostasis is vital for plant development, yet whether cells can actively reprogram organelle communication to restore plastid function when essential protease components fail remains unclear. Using a forward genetic suppressor screen in Arabidopsis, we identify loss of the mitochondria-associated protein FRIENDLY MITOCHONDRIA (FMT) as a strong suppressor of the virescent and growth-retarded clpc1 mutant, which lacks the major chloroplast Clp chaperone ClpC1. Suppression is highly specific and occurs independently of GUN1-mediated retrograde signaling. Integrated multi-omics analyses reveal that clpc1 and fmtclpc1 represent two distinct organelle signaling states. In clpc1, loss of ClpC1 triggers a plastid stress state characterized by repression of photosynthesis-associated transcription factors, induction of plastid metabolic stress markers, and impaired proteolytic activity. By contrast, loss of FMT shifts the system into a recovery state despite persistent mitochondrial clustering. Mechanistically, FMT negatively regulates CLPC2, a ClpC1 paralog, and fmt-mediated rescue results from CLPC2 derepression. Moderately elevated ClpC2 restores in vivo proteolysis, as evidenced by recovery of PAA2 substrate turnover, normalization of chloroplast ultrastructure, and reactivation of photosynthesis-related gene expression. Transcriptomic and proteomic profiling further reveal coordinated remodeling of nuclear gene expression and chloroplast protein investment in the recovery state, including reduced cytosolic folding stress and selective induction of jasmonic acid- and salicylic acid-associated signaling networks. Genetic analyses establish that REC1 and REC2 are required for full CLPC2 induction and phenotypic recovery. Together, our findings uncover a latent inter-organelle compensatory mechanism in which mitochondrial perturbation reprograms nuclear gene expression to restore chloroplast proteostasis when ClpC1 function is compromised.

plant biology↗

bioRxiv2026

Structural basis for dimerization, catalytic regulation, and substrate selectivity in S9D proteases

S9 proteases are widely distributed across the tree-of-life and play essential roles in protein processing. However, the structural and mechanistic basis for protease activity in the S9D subfamily has remained unknown. Here, we report the first high-resolution cryo-EM structures of an S9D protease, chloroplast glutamyl endopeptidase (CGEP) from Arabidopsis thaliana, expressed in plants and bacteria. CGEP adopts a dimeric architecture stabilized by two distinct interfaces: hydrophobic interactions between catalytic domains and an interdomain {beta}-sheet linking the cap and catalytic domains. These interactions create a rigid scaffold that supports a hinge loop, which acts as a steric gate to restrict substrate access and confine catalytic activity to the closed conformation. Unlike S9A-B-C proteases, CGEP maintains an intact catalytic triad in both open and closed states, relying on hinge-loop gating rather than catalytic disruption for regulation. Structural analysis and mutagenesis reveal that the hinge loop forms a conserved pocket favoring glutamate side chains, explaining CGEPs strong glutamate preference at cleavage sites. Together, these findings uncover a unique regulatory paradigm for S9D proteases and provide a structural framework for understanding substrate selectivity and dimerization. Significance statementThis study provides the first structural and mechanistic insights into plant S9D proteases, revealing a unique regulatory paradigm that combines hinge-loop gating with substrate-specific recognition. By uncovering how CGEP maintains catalytic integrity while restricting activity to the closed conformation and explaining its strong glutamate preference, these findings advance our understanding of protease diversity and open new avenues for engineering proteases with tailored specificity for agricultural and biotechnological applications.

biochemistry↗

bioRxiv2023

The Zea mays PeptideAtlas; a new maize community resource

We developed the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize were collected from ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds, including the inbred lines B73 and W22, many hybrids and their respective parents. Samples were collected from field trials, controlled environmental conditions, a range of (a)biotic conditions and different tissues, cell types and subcellular fractions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of the proteins (one isoform per protein coding gene) in the most recent B73 nuclear genome annotation (v5). Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other searched B73 genome annotations will aid to improve maize genome annotation. We also illustrate high confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical and biological metadata. This new PeptideAtlas is integrated with community resources including MaizeGDB at https://www.maizegdb.org/ and a peptide track in JBrowse. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/572651v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1ec9005org.highwire.dtl.DTLVardef@1e35f34org.highwire.dtl.DTLVardef@7f5b2corg.highwire.dtl.DTLVardef@13acefd_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2023

Converging paths: Harnessing ensemble modelling to predict human wild pig conflict risk zones in Tamil Nadu, India

Growing human populations and human activity intensify human-wildlife conflicts, particularly with wild pigs (Sus scrofa), necessitating consideration of both human and wildlife requirements. This complexity demands a comprehensive assessment of causes, impacts, and mitigation strategies for such conflicts. In order to address these issues, we conducted studies across the forest divisions of Tamil Nadu by collecting secondary data on conflicts from 2016 to 2021. Out of the 3301 incidents we collected, 94.4% were specifically related to crop damage and occurred mostly during the month of December, followed by November. Dharmapuri Forest Division was found to be the highest contributor to overall conflicts. Temporal analysis revealed conflict peaks in December, followed by November and September. Using ensemble modelling we predicted a conflict risk zone of approximately 49,223 km2, which represents 37.8% of the total area of Tamil Nadu. Variables like human modification index and mean annual temperature had the highest contribution to model performance. Our models projections indicate that areas with cultivated lands in close proximity to the fringes of forests, especially in regions where there is a greater degree of human modification, are associated with heightened levels of conflict risk. This study provides a concise overview of a comprehensive study on human-wild pig conflict, encompassing an exploration of conflict triggers and ecological impacts in the state of Tamil Nadu. The study offers a comprehensive roadmap for managing human-wild pig conflicts in Tamil Nadu, highlighting key triggers, ecological impacts, and conflict risk factors.

ecology↗

bioRxiv2023

Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome

This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying [~]0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the dark proteome. This dark proteome is highly enriched for certain (e.g. CLE, CEP, IDA, PSY) but not other (e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life (e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.

plant biology↗

bioRxiv2022

Differential Boric Acid and Water Transport in Type I and Type II Pores of Arabidopsis Nodulin 26-Intrinsic Protein

Nodulin-26 intrinsic proteins (NIPs) are plant-specific multifunctional aquaporin-like channels that are phylogenetically and structurally segregated into three subfamilies: NIP I, II, and III. Each subfamily has a characteristic selectivity filter sequence (the "aromatic-arginine" region, or ar/R) that controls substrate transport specificity based on steric constraints, hydrophobicity, and the spatial orientation of hydrogen bonding moieties. All three NIP subfamilies transport metalloid hydroxides, both beneficial as well as toxic, but with different selectivities. Here we investigated the B, As, and water selectivity of representative Arabidopsis thaliana NIP I and II proteins as well as their ar/R mutants in transport assays as well as through B complementation analysis in the B sensitive nip5;1 mutant background. All NIP proteins, and their ar/R mutants, showed equal permeability to arsenite, but showed differences in boric acid and aquaporin activities that was linked to the amino acid at the helix 2 (H2) position of the ar/R filter (Ala for NIP II and Trp for NIP I). The presence of an alanine at this position in NIP II proteins enhances boric acid permeability and drastically reduces the aquaporin/water permeability of the channel. A NIP II structural model generated from the AlphaFold2 resource and evaluated by MD simulation shows that the alanine results in a wider ar/R pore that accommodates the trigonal boric acid molecule and may allow gating of the pore in a manner that affects water permeability. In contrast, NIP I proteins adopt a more classical aquaporin/glyceroporin arrangement in the ar/R that allows metalloid permeability, although with greater selectivity, as well as permeation by water.

biochemistry↗

bioRxiv2020

The Arabidopsis thaliana NIP2;1 Lactic Acid Channel promotes Plant Survival Under Low Oxygen Stress

Under anaerobic stress Arabidopsis thaliana induces the expression of a collection of core hypoxia genes that encode proteins associated with an adaptive response. Included in these core hypoxia genes is NIP2;1, which encodes a member of the "Nodulin-like Intrinsic Protein" (NIP) subgroup of the aquaporin superfamily of membrane channel proteins. Under normal growth, NIP2;1 expression is limited to the "anoxia core" region of the root stele, but shows substantial induction in response to low oxygen stress (as high as 1000-fold by 2-4 hr of hypoxia challenge), and accumulates in all root tissues. During hypoxia, NIP2;1-GFP, accumulates on the cell surface by 2 hr and then is distributed between the cell surface and internal membranes during sustained hypoxia, and remains elevated in root tissues through 4 hrs of reoxygenation recovery. T-DNA insertional mutant nip2;1 plants show elevation of lactic acid within root tissues, and a reduced efflux of lactic acid and acidification of the external medium. Together with previous biochemical evidence demonstrating that NIP2;1 has lactic acid permease activity, the present work supports the hypothesis that the protein facilitates the release of cellular lactate to the rhizosphere to prevent lactic acid toxicity. In support of this, nip2;1 plants show poorer survival to argon-induced hypoxia stress. Nip2;1 mutant plants also show elevated expression of ethanolic fermentation transcripts, as well as reduced expression the lactate metabolic enzyme GOX3, suggesting that the altered efflux of lactate through NIP2;1 regulates other pyruvate and lactate metabolism pathways. One-sentence SummaryThe NIP2;1 lactic acid permease is necessary for an optimum response to low oxygen stress through the release of lactate from roots during hypoxia stress.

plant biology↗