This study aimed to establish a novel BRCA1 mutant cell line from Chinese hamster V79 cells and clarify the role of BRCA1 in the DNA damage response (DDR) by comparison with a BRCA2 mutant line, V-C8. Using CRISPR/Cas9 editing, we generated a hypomorphic BRCA1 mutant, designated B1-21, carrying a 27-bp in-frame deletion in exon 4. This mutation deletes nine amino acids within the RING domain. B1-21, V79, and V-C8 cells were analyzed for DDR phenotypes. Both mutants showed impaired RAD51 foci formation, defective homologous recombination repair, and increased sensitivity to DNA-damaging agents. B1-21 cells were particularly sensitive to camptothecin and the PARP inhibitor NU1025, whereas V-C8 cells showed higher sensitivity to etoposide, cisplatin, mitomycin C, and bleomycin. Although γH2AX and FANCD2 focus responses were similar between V79 and B1-21, RAD51 recruitment was only partially reduced in B1-21 and completely absent in V-C8. B1-21 also displayed chromosomal instability (19-20 chromosomes), while V79 and V-C8 maintained a stable karyotype. After gamma irradiation, V-C8 cells accumulated substantially more chromatid-type aberrations and retained unrepaired chromatin longer than B1-21. Neither mutant showed normal RAD51 foci formation, radiation-induced sister chromatid exchange or an effective G2/M checkpoint arrest, unlike wild-type cells. Mitotic index measurements further confirmed checkpoint failure: V79 cells suppressed mitotic entry after irradiation, while B1-21 and V-C8 continued to enter mitosis, with V-C8 showing the most complete checkpoint breakdown. These findings indicate that partial disruption of the BRCA1 RING domain results in a hypomorphic phenotype with impaired homologous recombination, defective checkpoint control, and enhanced genotoxic sensitivity. The isogenic BRCA1 and BRCA2 mutant V79 lines offer a valuable model for dissecting DDR pathway differences and developing mutation-specific therapeutic strategies targeting BRCA-mutant cancers.

The nuclear pore complex controls the movement of proteins into and out of the nucleus, allowing cells to regulate protein localization and abundance. This process influences how organisms respond to environmental stimuli. Components of the nuclear pore complex, including the NUP107-160 sub-complex, NUP133, NUP85, and NENA, are required for root nodulation and arbuscular mycorrhization in Lotus japonicus. However, the specific role of these nucleoporins in symbiotic signaling was poorly understood. Through reverse genetics, we discovered that NUP133 is also required for symbiosis in Medicago truncatula, although the mutant phenotypes were less pronounced than in Lotus. Overexpression of the symbiotic ion channels Medicago DMI1 and Lotus Castor and Pollux in the Lotus Ljnup133, Ljnup85, and Ljnena mutants partially alleviated the nodulation defects. Notably, in NUP107-160 sub-complex mutants of Lotus and Medicago, the accumulation of GFP-labeled Pollux and DMI1 on the inner nuclear membrane was reduced, indicating the NUP107-160 sub-complex plays a key role in regulating the distribution of DMI1 and Pollux on the nuclear envelope. This highlights the extreme sensitivity of nodulation in Lotus to changes in the abundance of Pollux on the inner nuclear membrane. In contrast, Medicago appears to exhibit greater tolerance to alterations in the distribution of DMI1 on the nuclear envelope.

Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device's capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, and stress-associated phenomena such as microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host-microbe interaction research.

Nijmegen Breakage Syndrome (NBS) is a rare autosomal recessive disorder characterized by chromosomal instability, immunodeficiency, radiosensitivity, and a strong predisposition to lymphoid malignancies. It is caused by mutations in the NBN gene encoding nibrin (NBS1) protein, a core component of the MRE11-RAD50-NBS1 (MRN) complex that senses DNA double-strand breaks (DSBs) and coordinates DNA damage response, including ATM activation. Despite the importance of NBS1, in the Chinese hamster system, which offers significant advantages in radiation biology and toxicology, no mutant lines deficient in the NBS1 gene have been isolated. In this study, we generated two novel NBS1 mutant Chinese hamster cell lines using CRISPR/Cas9, each carrying distinct NBN mutations leading to either null or hypomorphic mutations. These mutants exhibited growth retardation, marked sensitivity to ionizing radiation and various DNA damaging agents and elevated radiation induced chromosomal aberrations, recapitulating key NBS phenotypes. Notably, NBS1 mutant cells displayed pronounced hypersensitivity to ionizing radiation when co-treated with an ATR inhibitor, but not with a DNA-PK inhibitor. The ATR inhibitor also markedly sensitized NBS1 mutants to Etoposide, suggesting that ATR functions as a compensatory pathway in the absence of functional NBS1 during specific types of DNA damage. Collectively, our findings establish valuable NBS1-deficient Chinese hamster cell models that expand understanding of NBS1 function and highlight their utility for investigating DNA repair deficiencies and developing targeted therapeutic approaches for chromosomal instability disorders and cancers with NBS1 mutations.

The two primary DNA double-strand break (DSB) repair pathways, non-homologous end joining (NHEJ) and homologous recombinational repair (HRR), play crucial roles in determining radiosensitivity throughout the cell cycle. Our study investigated mechanisms underlying cell cycle-dependent radiosensitivity following exposure to accelerated charged particles in DSB signaling and repair-deficient CHO mutant cell lines. We confirmed NHEJ-deficient V3 cells exhibit hyper-radiosensitivity across all phases, while HRR-deficient 51D1 cells display increased sensitivity in the typically radioresistant S/G2 phase following X- and gamma-rays. Exposures to accelerated 290 MeV/n C-12 and 500 MeV/n Fe-56 ions induced complex DNA damage that was not fully repaired by either pathway, leading to increased cell killing. HRR-deficient cells exhibited higher relative biological effectiveness (RBE) values for cell killing in G1 and S and levels of chromatid-type chromosomal aberrations were higher in HRR-deficient cells. Additionally, impaired G2-phase checkpoint activation in HRR-deficient cells contributed to mitotic entry with unresolved DNA damage. Our findings suggest that charged particles produce complex lesions that require coordinated repair by both major DSB repair pathways, and disruption of either pathway leads to increased radiosensitivity.

Sulfoglycolipid, α-sulfoquinovosyl-acylpropanediol (SQAP) is a novel veterinary radiosensitizer, which is known to cause angiogenesis alteration and sensitizes hypoxic tumors in the in vivo animal model. We examined the SQAP radio/chemo-sensitization mechanisms from DNA repair with canine cancer cell lines and Chinese hamster cell lines. Previous studies have shown that SQAP radiosensitization was limited to in vivo xenograft models, but we found SQAP sensitized cells to radiation in vitro cell culture system. SQAP sensitized canine osteosarcoma and melanoma cell lines to gamma-ray irradiation in normoxia or hypoxia conditions. This result suggested that SQAP was expected to affect the repair of DNA damage induced by ionizing radiation and enhanced cellular radiosensitivity. To further identify potential mechanisms of radiosensitization, we utilized several assays to determine DNA repair inhibition by SQAP. SQAP treatment inhibited NHEJ and HR activity measured by EJ5-GFP and DR-GFP assays. SQAP treatment reduced the spontaneous sister chromatid exchange formation in CHO wild type and EM9 (XRCC1 mutant). On the other hand, 51D1 (rad51d mutant, homologous recombination (HR) repair deficient) showed no reduction. In vitro topoisomerase assay revealed SQAP disrupted topoisomerase I and II alpha activities. SQAP sensitized series of chemotherapeutic agents including doxorubicin, carboplatin, bleomycin, camptothecin, etoposide, methyl methanesulfonate, cisplatin, mitomycin C, and Taxol in canine tumor cells and V79 cells. These results suggest that broad inhibition of DNA repair may play a role in SQAP induced radiosensitization and chemosensitization.

Taxol is an antitumor agent that arrests cells in the late G2 and M phases of the cell cycle. Our previous research demonstrated that PARP inhibition enhances Taxol-induced cell death via oxidative stress and free radical production. In this study, we hypothesized that the inhibiting DNA damage response (DDR) kinases would further increase Taxol cytotoxicity by impairing the repair of Taxol-induced DNA damage. We found that inhibition of PI3K-like DDR kinases enhanced Taxol-induced apoptosis through caspase-3 activation. We used Chinese hamster V79 cells and their ATM, ATR, and Ku80-deficient mutants which exhibited hypersensitivity to Taxol. Pharmacological inhibitors, KU55933 (ATM), NU7441 (DNA-PK), and VE821 (ATR), also sensitized V79, CHO, and U2OS human cancer cells to Taxol. This sensitization was associated with increased apoptosis, confirmed by sub-G1 analysis and caspase-3/7 activity assays. Interestingly, MCF7 cells, which lack caspase-3, did not show enhanced sensitivity to Taxol under DDR inhibition. In contrast, MCF7-C3 cells, with restored caspase-3 expression, exhibited significant apoptosis and sensitization, confirming a caspase-3 dependent mechanism. These findings suggest that ATM, ATR, and DNA-PK not only facilitate DNA repair but also suppress Taxol-induced apoptosis via caspase-3. Their inhibition may represent a promising strategy to boost their efficacy of Taxol and potentially enhance responses to radiation therapy through combined targeting of mitotic stress and DDR pathways.

AbstractIncreasing biological nitrogen (N) fixation (BNF) in maize production could reduce the environmental impacts of N fertilizer use, but reactive N in the rhizosphere of maize limits the BNF process. Using non-transgenic methods, we developed gene-edited strains of Klebsiella variicola (Kv137-2253) and Kosakonia sacchari (Ks6-5687) bacteria optimized for root-associated BNF and ammonium excretion in N-rich conditions. The aim of this research was to elucidate the mechanism of action of these strains. We present evidence from in vitro, in planta and field experiments that confirms that our genetic remodeling strategy derepresses BNF activity in N-rich systems and increases ammonium excretion by orders of magnitude above the respective wildtype strains. BNF is demonstrated in controlled environments by the transfer of labeled 15N2 gas from the rhizosphere to the chlorophyll of inoculated maize plants. This was corroborated in several 15N isotope tracer field experiments where inoculation with the formulated, commercial-grade product derived from the gene-edited strains (PIVOT BIO PROVEN® 40) provided on average 21 kg N ha-1 to the plant by the VT-R1 growth stages. Data from small-plot and on-farm trials suggest that this technology can improve crop N status pre-flowering and has potential to mitigate the risk of yield loss associated with a reduction in synthetic N fertilizer inputs.

XRCC8 is a member of the X-ray cross-complementing (XRCC) family, whose responsible gene has not been identified. Previous studies suggested ATM and other genes were potential candidates for XRCC8, but this was not confirmed. In this study, we characterized three V79-derived XRCC8 mutant cells: V-C4, V-E5, and V-G8. Western blot analysis showed reduced expression of the ATM protein in three XRCC8 mutants, and radiation-induced phosphorylated ATM foci were not detected by fluorescence immunocytochemistry. Both ATM knockout cells and XRCC8 mutants exhibited hypersensitivity to camptothecin. Through a cell fusion-based complementation test, we found that XRCC8 mutants were complemented by ATM-proficient cells, but not by ATM knockout cells, in terms of camptothecin sensitivity. Comprehensive sequencing of the ATM genome in XRCC8 mutants revealed unique mutations in each mutant. These results suggest that XRCC8 mutants carry ATM mutations, and their ATM is not properly functional, despite protein expression being detected. This is similar to missense mutations in some Ataxia Telangiectasia patients.

Chinese hamster-derived cell lines including Chinese hamster lung fibroblasts (V79) have been used as model somatic cell lines in radiation biology and toxicology research for decades and have been instrumental in advancing our understanding of DNA damage response (DDR) mechanisms. Whereas many mutant lines deficient in DDR genes have been generated more than over decades, several key DDR genes such as ATM and ATR have not been established in the Chinese hamster system. Here, we transfected CRISPR/Cas9 vectors targeting Chinese hamster ATM or ATR into V79 cells and investigated whether the isolated clones had the characteristics reported in human and mouse studies. We obtained two clones of ATM knockout cells containing an insertion or deletions in the targeted locus. The ATM knockouts with no detectable ATM protein expression exhibited increased sensitivity to radiation and DNA double strand break inducing agents, cell cycle checkpoint defects and defective chromatid break repair. These are all characteristics of defective ATM function. Among the obtained ATR cells, which contained mutations in both ATR alleles while maintaining normal levels of ATR protein expression, one clone exhibited hypersensitivity to UV and replication stress agents. In the present study, we successfully established CRISPR-Cas9 derived ATM knockout cells. We couldn't knock out the ATR gene but obtained ATR mutant cells. Our results showed that Chinese hamster origin ATM knockout cells and ATR mutant cells could be useful tools for further research to reveal oncogenic functions and effects of developing anti-cancer therapeutics.

Here we report that simultaneous inhibition of the three primary DNA damage recognition PI3 kinase-like kinases (PIKKs) —ATM, ATR, and DNA-PK— induces severe combinatorial synthetic lethality in mammalian cells. Utilizing Chinese hamster cell lines CHO and V79 and their respective PIKK mutants, we evaluated effects of inhibiting these three kinases on cell viability, DNA damage response, and chromosomal integrity. Our results demonstrate that while single or dual kinase inhibition increased cytotoxicity, inhibition of all three PIKKs results in significantly higher synergistic lethality, chromosomal aberrations, and DNA double-strand break (DSB) induction as calculated by their synergy scores. These findings suggest that the overlapping redundancy of ATM, ATR, and DNA-PK functions is critical for cell survival, and their combined inhibition greatly disrupts DNA damage signaling and repair processes, leading to cell death. This study provides insights into the potential of multi-targeted DDR kinase inhibition as an effective anticancer strategy, necessitating further research to elucidate underlying mechanisms and therapeutic applications.

Radiation exposure poses a significant threat to cellular integrity by inducing DNA damage through the generation of free radicals and reactive oxygen species. Ascorbic acid, particularly its derivative Palmitoyl Ascorbic Acid 2-Glucoside (PA2G), has demonstrated remarkable radioprotective properties. While previous research focused on its pre-irradiation application, this study explores the post-irradiation radiomitigation potential of PA2G. Our findings reveal that post-irradiation treatment with PA2G enhances cell survival and accelerates DNA repair processes, particularly the non-homologous end-joining (NHEJ) repair pathway. Notably, PA2G treatment reduces the frequency of lethal chromosomal aberrations and micronuclei formation, indicating its ability to enhance the repair of complex DNA lesions. Furthermore, PA2G is shown to play a role in potentially lethal damage repair (PLDR). These radioprotective effects are specific to NHEJ and ATM pathways, as cells deficient in these mechanisms do not benefit from PA2G treatment. This study highlights PA2G as a versatile radioprotector, both pre- and post-irradiation, with significant potential for applications in radiation therapy and protection, offering new insights into its mechanism of action. Further research is required to elucidate the precise molecular mechanisms underlying PA2G's radiomitigation effects and its potential clinical applications.

PARP inhibitors inflict severe toxicity to homologous recombination (HR) repair deficient cells because DNA damages induced by PARP inhibition result in lethal DNA double strand breaks in the absence of HR repair during DNA replication. PARP inhibitors are the first clinically approved drugs designed for synthetic lethality. The synthetic lethal interaction of PARP inhibitors is not limited to HR repair deficient cells. We investigated radiosensitive mutants isolated from Chinese hamster lung origin V79 cells to identify novel synthetic lethal targets in the context of PARP inhibition. HR repair deficient BRCA2 mutant cells were used for positive control. Among tested cells, XRCC8 mutants presented hypersensitivity to PARP inhibitor, Olaparib. XRCC8 mutants showed elevated sensitivity to bleomycin and camptothecin similar to BRCA2 mutants. XRCC8 mutants presented an elevation of γ-H2AX foci formation frequency and S-phase dependent chromosome aberrations with Olaparib treatment. Enumerated damage foci following Olaparib treatment were observed to be elevated in XRCC8 as in BRCA2 mutants. Although this may suggest that XRCC8 plays a role in a similar DNA repair pathway as BRCA2 in HR repair, XRCC8 mutants presented functional HR repair including proper Rad51 foci formation and even elevated sister chromatid exchange frequencies with PARP inhibitor treatment. For comparison, RAD51 foci formation was suppressed in HR repair deficient BRCA2 mutants. Additionally, XRCC8 mutants did not display delayed mitotic entry with PARP inhibitors whereas BRCA2 mutants did. XRCC8 mutant cell line has previously been reported as possessing a mutation in the ATM gene. XRCC8 mutants displayed maximum cytotoxicity to ATM inhibitor among tested mutants and wild type cells. Furthermore, the ATM inhibitor sensitized XRCC8 mutant to ionzing radiation, however, XRCC8 mutant V-G8 expressed reduced levels of ATM protein. The gene responsible for XRCC8 phenotype may not be ATM but highly associated with ATM functions. These results suggest that XRCC8 mutation is a target for PARP inhibitor-induced synthetic lethality in HR repair independent manner via the disruption of cell cycle regulation. Our findings expand the potential application of PARP inhibitors in tumors lacking DNA damage responding genes other than HR repair, and further investigation of XRCC8 may contribute to this research.

Taxol is an antitumor drug derived from the bark of the Pacific Yew tree that inhibits microtubule disassembly, resulting in cell cycle arrest in late G2 and M phases. Additionally, Taxol increases cellular oxidative stress by generating reactive oxygen species. We hypothesized that the inhibition of specific DNA repair machinery/ mechanisms would increase cellular sensitivity to the oxidative stress capacity of Taxol. Initial screening using Chinese hamster ovary (CHO) cell lines demonstrated that base excision repair deficiency, especially PARP deficiency, caused cellular Taxol hypersensitivity. Taxane diterpenes-containing Taxus yunnanensis extract also showed hypertoxicity in PARP deficient cells, which was consistent with other microtubule inhibitors like col-cemid, vinblastine, and vincristine. Acute exposure of 50 nM Taxol treatment induced both significant cyto-toxicity and M-phase arrest in PARP deficient cells, but caused neither significant cytotoxicity nor late G2-M cell cycle arrest in wild type cells. Acute exposure of 50 nM Taxol treatment induced oxidative stress and DNA damage. The antioxidant Ascorbic acid 2 glucoside partially reduced the cytotoxicity of Taxol in PARP deficient cell lines. Finally, the PARP inhibitor Olaparib increased cytotoxicity of Taxol in wild type CHO cells and two human cancer cell lines. Our study clearly demonstrates that cytotoxicity of Taxol would be enhanced by inhibiting PARP function as an enzyme implicated in DNA repair for oxidative stress.

Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them.

Sulfoquinovosyl acylpropanediol (SQAP; a synthetic derivative of the sulfoglycolipid natural product sulfoquinovosyl acylglycerol, SQAG), has anti-tumor and radiosensitizing activities in tumor xenograft mouse models. Here, we have studied the PARP inhibitory activity of SQAP and synthetic lethality in BRCA2-deficient cells. In initial screening studies with DNA repair-deficient Chinese hamster ovary cells, homologous recombination repair-deficient cell lines showed increased sensitivity to SQAP, compared to wild-type cells or other DNA repair deficient mutants. Chinese hamster lung V79 cells and the derivative cell lines V-C8 (BRCA2-deficient) and V-C8 + BRCA2 gene corrections were used to test the role of BRCA2 in SQAP cytotoxicity. The findings were confirmed in studies of the human colon cancer cell lines DLD-1 and its BRCA2-knockout derivative. SQAP inhibited the enzymes poly(ADP-ribose) polymerase (PARP) and poly(ADP-ribose) glycohydrolase (PARG). SQAP pretreatment decreased H2O2induced poly(ADP-ribose) formation in V79 cells. SQAP caused DNA double-strand breaks and chromosome aberrations in V79 BRCA2-mutated cells but did not affect cells in the G2 phase. We have demonstrated that SQAP induces synthetic lethality in BRCA2-deficient Chinese hamster-derived cells via its effects on poly(ADP-ribose) metabolism, motivating further examination of its therapeutic potential, especially against tumors that are deficient in homologous recombination repair due to mutations in BRCA2 or other genes.

Symbioses between angiosperms and rhizobia or arbuscular mycorrhizal fungi are controlled through a conserved signaling pathway. Microbe-derived, chitin-based elicitors activate plant cell surface receptors and trigger nuclear calcium oscillations, which are decoded by a calcium/calmodulin-dependent protein kinase (CCaMK) and its target transcription factor interacting protein of DMI3 (IPD3). Genes encoding CCaMK and IPD3 have been lost in multiple non-mycorrhizal plant lineages yet retained among non-mycorrhizal mosses. Here, we demonstrated that the moss Physcomitrium is equipped with a bona fide CCaMK that can functionally complement a Medicago loss-of-function mutant. Conservation of regulatory phosphosites allowed us to generate predicted hyperactive forms of Physcomitrium CCaMK and IPD3. Overexpression of synthetically activated CCaMK or IPD3 in Physcomitrium led to abscisic acid (ABA) accumulation and ectopic development of brood cells, which are asexual propagules that facilitate escape from local abiotic stresses. We therefore propose a functional role for Physcomitrium CCaMK-IPD3 in stress-associated developmental reprogramming.

The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor , the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO4), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor . Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.

Background Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula , in response to rhizobial signals that trigger the formation of root nodules. Results We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis -regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. Conclusions Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.

Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.