A catalogue of proteins released from Asaia bogorensis under two growth conditions

Bacterial secretion systems are essential for growth and responsible for a plethora of functions, ranging from nutrient acquisition to biofilm formation, and pathogenesis. Bacteria use Type II secretion systems (T2SS) to transport folded proteins from the periplasm outside of the cell in a two-step process. Opportunistic pathogens often secrete virulence factors through this pathway. In contrast, the Type I secretion system transports proteins across both the inner and outer membranes in a single step. The Type 4 secretion system also transports substrates across the entire cell envelope. In many instances, it also translocates substrates directly into target cells. Researchers have utilized the Gram-negative bacterium Asaia bogorensis for paratransgenesis. The bacterium was engineered to secrete anti-Plasmodium effector peptides to target and destroy the Plasmodium parasites that cause malaria in the mosquito vector through the T2SS. Here we identify a catalogue of proteins released by..., Collection of samples 
Asaia bogorensis SF2.1 was grown in mannitol broth (0.5% yeast extract, 0.3% peptone, 0.5% mannitol (w/v)) to saturation in triplicate. At this time 100 μL of each culture was placed onto Davis minimal agar (0.7% dipotassium phosphate, 0.2% monopotassium phosphate, 0.05% sodium citrate, 0.01% magnesium sulfate, 0.1% ammonium sulfate (w/v) with 15 g/L agar) supplemented with 10% glucose solution (v/v) as well as chocolate agar (Davis minimal media agar supplemented with 10% glucose solution (v/v) and 2.5% lysed defibrinated sheep blood (v/v)). After three days of growth at 30°C, all samples and secretions were gently scraped from the plates for 30 seconds in 1 mL of Davis minimal broth using a glass scraper and immediately transferred to microcentrifuge tubes. All samples were centrifuged at 9,000 xg for 5 minutes, and supernatants were transferred immediately to fresh tubes and saved as the secreted samples.
Sample preparation
Seventy-five μL of each supernat..., , # Data from: A catalogue of proteins released from Asaia bogorensis under two growth conditions

[https://doi.org/10.5061/dryad.4mw6m90nd](https://doi.org/10.5061/dryad.4mw6m90nd)

## Description of the data and file structure

### Files and variables

#### File: 5.zip

**Description:**  This is a scaffold file containing all potentially secreted proteins identified using LC-MS/MS from A. bogorensis. In this study, samples were grown under two conditions, chocolate media agar (lysed red blood cell agar) and minimal media agar. 

**Samples and sample abbreviations**: Headings Chocolate and Minimal refer to the growth media from which all bacterial proteins were collected. Subheadings Choc 1, 2, etc, refer to the individual replicates for each collection. \"Chocolate and Minimal No\" refers to the negative control samples. On these plates, no bacteria were grown, but proteins were collected in the same method as all other samples. 

Each sample (Choc 1, Choc 2, Choc 3, Choc No, Min 1, Mi...,

细菌分泌系统对细菌生长至关重要，同时承担着从营养获取到生物被膜形成乃至致病过程在内的诸多功能。细菌采用II型分泌系统（Type II secretion system, T2SS），通过两步过程将周质中的折叠蛋白转运至细胞外。机会致病菌常通过该途径分泌毒力因子。与之相对，I型分泌系统（Type I secretion system）可一步完成跨内膜与外膜的蛋白转运。IV型分泌系统（Type 4 secretion system）同样可介导底物跨越完整的细菌细胞包膜，在诸多情况下还能直接将底物转位至靶细胞内。

研究人员曾将革兰氏阴性细菌（Gram-negative bacterium）博戈里尼阿萨伊菌（Asaia bogorensis）用于副转基因（paratransgenesis）研究。该工程菌经改造后可通过II型分泌系统分泌抗疟原虫效应肽，以靶向并杀灭蚊媒体内引发疟疾的疟原虫。本研究鉴定得到了由[...]释放的蛋白目录。

样本采集：将博戈里尼阿萨伊菌SF2.1菌株接种于甘露醇肉汤（0.5%酵母提取物、0.3%蛋白胨、0.5%甘露醇，质量体积比）中，进行三次重复培养至饱和。随后取每份培养液100 μL，涂布于添加10%葡萄糖溶液（体积比）的戴维斯基础琼脂平板（0.7%磷酸氢二钾、0.2%磷酸二氢钾、0.05%柠檬酸钠、0.01%硫酸镁、0.1%硫酸铵，质量体积比，琼脂含量15 g/L），以及巧克力琼脂平板（即在戴维斯基础琼脂中添加10%葡萄糖溶液（体积比）与2.5%裂解脱纤维羊血（体积比））。于30℃培养3天后，使用玻璃刮棒在1 mL戴维斯基础肉汤中轻柔刮取平板上的所有样本与分泌产物，持续30秒，随后立即转移至微量离心管中。所有样本经9000×g离心5分钟，上清液即刻转移至新管中，作为分泌样本保存。

样本制备：每份上清液75 μL[...]。

# 数据来源：两种培养条件下博戈里尼阿萨伊菌释放的蛋白组目录
DOI: https://doi.org/10.5061/dryad.4mw6m90nd

## 数据与文件结构说明

### 文件与变量

#### 文件：5.zip
**描述**：本支架文件包含了通过液相色谱-串联质谱（Liquid Chromatography-Tandem Mass Spectrometry, LC-MS/MS）鉴定得到的博戈里尼阿萨伊菌所有潜在分泌蛋白。本研究中，样本分别于两种培养基中培养：巧克力琼脂平板（裂解红细胞琼脂平板）与基础琼脂平板。
**样本与样本缩写**：表头"Chocolate"与"Minimal"指代采集细菌蛋白的生长培养基；子表头"Choc 1、2等"指代每次采集的独立生物学重复。"Chocolate and Minimal No"指代阴性对照样本：该平板未接种细菌，但采用与其余样本一致的方法收集蛋白。
每个样本（Choc 1、Choc 2、Choc 3、Choc No、Min 1、Mi[...]）