A MAP Kinase Kinase Interacts with SymRK and Regulates Nodule Organogenesis in Lotus japonicus

The symbiosis receptor kinase, SymRK, is required for root nodule development. A SymRK-interacting protein (SIP2) was found to form protein complex with SymRK in vitro and in planta. The interaction between SymRK and SIP2 is conserved in legumes. The SIP2 gene was expressed in all Lotus japonicus tissues examined. SIP2 represents a typical plant mitogen-activated protein kinase kinase (MAPKK) and exhibited autophosphorylation and transphosphorylation activities. Recombinant SIP2 protein could phosphorylate casein and the Arabidopsis thaliana MAP kinase MPK6. SymRK and SIP2 could not use one another as a substrate for phosphorylation. Instead, SymRK acted as an inhibitor of SIP2 kinase when MPK6 was used as a substrate, suggesting that SymRK may serve as a negative regulator of the SIP2 signaling pathway. Knockdown expression of SIP2 via RNA interference (RNAi) resulted in drastic reduction of nodules formed in transgenic hairy roots. A significant portion of SIP2 RNAi hairy roots failed to form a nodule. In these roots, the expression levels of SIP2 and three marker genes for infection thread and nodule primordium formation were downregulated drastically, while the expression of two other MAPKK genes were not altered. These observations demonstrate an essential role of SIP2 in the early symbiosis signaling and nodule organogenesis

A MAP kinase kinase interacts with SymRK and regulates nodule organogenesis in Lotus japonicus

The symbiosis receptor kinase, SymRK, is required for root nodule development. A SymRK-interacting protein (SIP2) was found to form protein complex with SymRK in vitro and in planta. The interaction between SymRK and SIP2 is conserved in legumes. The SIP2 gene was expressed in all Lotus japonicus tissues examined. SIP2 represents a typical plant mitogen-activated protein kinase kinase (MAPKK) and exhibited autophosphorylation and transphosphorylation activities. Recombinant SIP2 protein could phosphorylate casein and the Arabidopsis thaliana MAP kinase MPK6. SymRK and SIP2 could not use one another as a substrate for phosphorylation. Instead, SymRK acted as an inhibitor of SIP2 kinase when MPK6 was used as a substrate, suggesting that SymRK may serve as a negative regulator of the SIP2 signaling pathway. Knockdown expression of SIP2 via RNA interference (RNAi) resulted in drastic reduction of nodules formed in transgenic hairy roots. A significant portion of SIP2 RNAi hairy roots failed to form a nodule. In these roots, the expression levels of SIP2 and three marker genes for infection thread and nodule primordium formation were downregulated drastically, while the expression of two other MAPKK genes were not altered. These observations demonstrate an essential role of SIP2 in the early symbiosis signaling and nodule organogenesis

Whole genome sequencing reveals complexity in both HPV sequences present and HPV integrations in HPV-positive oropharyngeal squamous cell carcinomas

Abstract Background High risk human papillomaviruses (HPV) plays important roles in the development of cervical cancer, a number of other anogenital cancer and they are increasingly found in oropharyngeal squamous cell carcinoma (OPSCC), however there has not been comprehensive analysis about the role how these viruses play in the development of OPSCC. Methods To characterize the physical status of HPV within OPSCC and to determine the effect this has throughout the host genome, we have performed 30-40X whole genome sequencing (WGS) on the BGI sequencing platform on 34 OPSCCs: 28 of which were HPV positive. We then examined the sequencing data to characterize the HPV copy number and HPV physical status to determine what effect they have on both HPV and human genome structural changes. Results WGS determined the HPV copy number across the viral genome. HPV copy number ranged from 1 copy to as high as 150 copies in each individual OPSCC. Independent of HPV copy number, most tumors had either a small or a very large deletion in the viral genome. We discovered that these deletions were the result of either HPV integration into the human genome or HPV-HPV sequence junctions. WGS revealed that ~ 70% of these tumors had HPV integrations within the human genome and HPV integration occurred independent of HPV copy number. Individual HPV integrations were found to be highly disruptive resulting in structural variations and copy number changes at or around the integration sites. Conclusions WGS reveals that there is a great complexity in both HPV sequences present and the HPV integrations events in HPV positive OPSCCs tumors. Thus HPV may be playing different roles in the development of different OPSCCs and this further challenge the HPV-driven carcinogenesis model first proposed for cervical cancer

A Ubiquitin Ligase of Symbiosis Receptor Kinase Involved in Nodule Organogenesis

The symbiosis receptor kinase (SymRK) is required for morphological changes of legume root hairs triggered by rhizobial infection. How protein turnover of SymRK is regulated and how the nodulation factor signals are transduced downstream of SymRK are not known. In this report, a SymRK-interacting E3 ubiquitin ligase (SIE3) was shown to bind and ubiquitinate SymRK. The SIE3-SymRK interaction and the ubiquitination of SymRK were shown to occur in vitro and in planta. SIE3 represents a new class of plant-specific E3 ligases that contain a unique pattern of the conserved CTLH (for C-terminal to LisH), CRA (for CT11-RanBPM), and RING (for Really Interesting New Gene) domains. Expression of SIE3 was detected in all tested tissues of Lotus japonicus plants, and its transcript level in roots was enhanced by rhizobial infection. The SIE3 protein was localized to multiple subcellular locations including the nuclei and plasma membrane, where the SIE3-SymRK interaction took place. Overexpression of SIE3 promoted nodulation in transgenic hairy roots, whereas downregulation of SIE3 transcripts by RNA interference inhibited infection thread development and nodule organogenesis. These results suggest that SIE3 represents a new class of E3 ubiquitin ligase, acts as a regulator of SymRK, and is involved in rhizobial infection and nodulation in L. japonicus

Revue des architectes français : organe corporatif paraissant les 1er et 15 de chaque mois

01 avril 19441944/04/01 (A3,N67)-1944/04/15 (A3,N68)

Genetic resiliency associated with dominant lethal TPM1 mutation causing atrial septal defect with high heritability

Analysis of large-scale human genomic data has yielded unexplained mutations known to cause severe disease in healthy individuals. Here, we report the unexpected recovery of a rare dominant lethal mutation in TPM1, a sarcomeric actin-binding protein, in eight individuals with large atrial septal defect (ASD) in a five-generation pedigree. Mice with Tpm1 mutation exhibit early embryonic lethality with disrupted myofibril assembly and no heartbeat. However, patient-induced pluripotent-stem-cell-derived cardiomyocytes show normal beating with mild myofilament defect, indicating disease suppression. A variant in TLN2, another myofilament actin-binding protein, is identified as a candidate suppressor. Mouse CRISPR knock-in (KI) of both the TLN2 and TPM1 variants rescues heart beating, with near-term fetuses exhibiting large ASD. Thus, the role of TPM1 in ASD pathogenesis unfolds with suppression of its embryonic lethality by protective TLN2 variant. These findings provide evidence that genetic resiliency can arise with genetic suppression of a deleterious mutation

Somatic variants in mesothelioma patients identified using BGISEQ-500 and HiSeq X Ten data.

<p>A summary of the somatic variants identified in 3 mesothelioma patient samples (patient ID: 9869, 11202 and 11398) using different sequencing platforms. The number of somatic SNV (<b>a</b>) and indels (<b>b</b>) identified using the BGISEQ-500 and HiSeq X Ten platforms in each patient. The somatic SNV (<b>c</b>) and indels (<b>d</b>) which were only called in one platform fall into three categories: i) identified as somatic in the other platform but with low evidence; ii) identified in the other platform but predicted as a germline variant; or iii) not identified in the other platform.</p

Number of germline and somatic variants identified in three mesothelioma samples using whole genome sequencing.

<p>The percentage of the germline variants identified in this study and reported in European population data from gnomAD are presented in brackets.</p

Average genome read depth using BGISEQ-500 and HiSeq X Ten data.

<p>The average whole-genome sequencing read depth for each platform (blue BGISEQ-500, yellow HiSeq X Ten), for each tumour (T) and normal (N) sample is displayed for three mesothelioma patients (9869, 11202 and 11398). Prior to variant calling sequence reads underwent quality filtering, and the subsequent average read depth remained similar between sequencing platforms, this is a more relevant measure of read depth as it represents the ‘usable’ portion of the sequencing data for detecting variants. The average quality-filtered sequencing read depth is indicated by the shaded bar.</p

Germline variants identified in three mesothelioma samples (patients: 9869, 11202 and 11398) using BGISEQ-500 and HiSeq X Ten data.

<p>The number of germline SNV (<b>a</b>) and indels (<b>b</b>) identified in each patient using the BGISEQ-500 and HiSeq X Ten platforms. We investigated germline SNV (<b>c</b>) and indels (<b>d</b>) which were only called in one platform and that fall into three categories: i) identified as germline in the other platform but with low evidence; ii) identified in the other platform but predicted as a somatic variant; or iii) not identified in the other platform. Across the 3 patients only 197,434 (1.85%) SNVs were truly unique to the HiSeq X Ten and not identified in the BGISEQ-500 (c). Similarly in the BGISEQ-500 platform only 38,236 SNVs (0.36% of the total) were truly unique to the BGISEQ-500, not called in the HiSeq X Ten data (c). The same pattern was observed for indels (d), only 3.23% were unique to HiSeq X Ten and 0.19% to BGISEQ-500.</p