From 05c8bca73fffeca7c577556665e57118bb92ad52 Mon Sep 17 00:00:00 2001 From: Angela Kranz <a.kranz@fz-juelich.de> Date: Sun, 3 Sep 2023 15:43:56 +0000 Subject: [PATCH] Update README.md --- README.md | 86 ++++--------------------------------------------------- 1 file changed, 6 insertions(+), 80 deletions(-) diff --git a/README.md b/README.md index 026a327..952fa74 100644 --- a/README.md +++ b/README.md @@ -2,91 +2,17 @@ -## Getting started +## Abstract / Summary -To make it easy for you to get started with GitLab, here's a list of recommended next steps. +The response of gene expression to oxygen limitation in the obligately aerobic acetic acid bacterium _Gluconobacter oxydans_ is not well understood in terms of the regulators involved. In this research, we focused on investigating a transcriptional regulator called GoxR (GOX0974), which stands as the sole representative of the fumarate-nitrate reduction regulator (FNR) family within this organism. Our findings suggest that GoxR contains an iron-sulfur cluster, implying its role as an oxygen sensor, akin to FNR. To identify the specific genes directly regulated by GoxR, we employed multiple methodologies, including a transcriptome comparison between a Δ_goxR_ mutant and the wild-type strain, as well as the detection of in vivo GoxR binding sites using chromatin affinity purification and sequencing (ChAP-Seq). -Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)! +Among the notable targets of GoxR were the _cioAB_ genes responsible for encoding a cytochrome bd oxidase with low affinity for oxygen, which GoxR repressed, and the pnt operon, which GoxR activated. The pnt operon encompasses genes for a transhydrogenase (_pntA1A2B_), an NADH-dependent oxidoreductase (GOX0313), and another oxidoreductase (GOX0314). Intriguingly, we discovered that GoxR remained active even in conditions with a high concentration of dissolved oxygen in the medium. -## Add your files +We propose a model in which the exceptionally high rates of respiration in _G. oxydans_, owing to periplasmic oxidations, result in an oxygen-limited cytoplasm and inadequate reoxidation of NAD(P)H within the respiratory chain. This leads to the inhibition of cytoplasmic carbohydrate degradation. GoxR-induced activation of the pnt operon facilitates rapid conversion between NADPH and NADH by the transhydrogenase, as well as NADH reoxidation through the GOX0313 oxidoreductase, via the reduction of acetaldehyde formed by pyruvate decarboxylase into ethanol. Indeed, under oxygen-restricted conditions, _G. oxydans_ produces small quantities of ethanol in a GoxR-dependent manner. -- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files -- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command: +## Citation +Schweikert S, Kranz A, Yakushi T, Filipchyk A, Polen T, Etterich H, Bringer S, Bott M. FNR-Type Regulator GoxR of the Obligatorily Aerobic Acetic Acid Bacterium _Gluconobacter oxydans_ Affects Expression of Genes Involved in Respiration and Redox Metabolism. Appl Environ Microbiol. 2021 May 11;87(11):e00195-21. doi: 10.1128/AEM.00195-21. PMID: 33741613; PMCID: PMC8208152. ``` -cd existing_repo -git remote add origin https://git.nfdi4plants.org/fzj_ibg-4/goxr_characterization.git -git branch -M main -git push -uf origin main -``` - -## Integrate with your tools - -- [ ] [Set up project integrations](https://git.nfdi4plants.org/fzj_ibg-4/goxr_characterization/-/settings/integrations) - -## Collaborate with your team - -- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/) -- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html) -- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically) -- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/) -- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html) - -## Test and Deploy - -Use the built-in continuous integration in GitLab. - -- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html) -- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/) -- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html) -- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/) -- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html) - -*** - -# Editing this README - -When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template. - -## Suggestions for a good README -Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information. - -## Name -Choose a self-explaining name for your project. - -## Description -Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors. - -## Badges -On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge. - -## Visuals -Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method. - -## Installation -Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection. - -## Usage -Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README. - -## Support -Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc. - -## Roadmap -If you have ideas for releases in the future, it is a good idea to list them in the README. - -## Contributing -State if you are open to contributions and what your requirements are for accepting them. - -For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self. - -You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser. - -## Authors and acknowledgment -Show your appreciation to those who have contributed to the project. -## License -For open source projects, say how it is licensed. -## Project status -If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers. -- GitLab